16-57657353-C-G

Variant names:

• chr16-57657353-C-G
• rs2305309
• NM_201525.4:c.1168-20C>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_201525.4(ADGRG1):​c.1168-20C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,464 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: ADGRG1 NM_201525.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.45
• Publications: 10 publications found

Genes affected

ADGRG1 (HGNC:4512): (adhesion G protein-coupled receptor G1) This gene encodes a member of the G protein-coupled receptor family and regulates brain cortical patterning. The encoded protein binds specifically to transglutaminase 2, a component of tissue and tumor stroma implicated as an inhibitor of tumor progression. Mutations in this gene are associated with a brain malformation known as bilateral frontoparietal polymicrogyria. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

ADGRG1 Gene-Disease associations (from GenCC):

• bilateral frontoparietal polymicrogyria

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen, G2P

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 16-57657353-C-G is Benign according to our data. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-57657353-C-G is described in CliVar as Likely_benign. Clinvar id is 3012129.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRG1	NM_201525.4	c.1168-20C>G		intron_variant	Intron 9 of 13	ENST00000562631.7	NP_958933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRG1	ENST00000562631.7	c.1168-20C>G		intron_variant	Intron 9 of 13	1	NM_201525.4	ENSP00000455351.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000797 AC: 2 AN: 250974 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000578

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1461464 Hom.: 0 Cov.: 38 AF XY: 0.00 AC XY: 0 AN XY: 727060

African (AFR) AF: 0.00 AC: 0 AN: 33474

American (AMR) AF: 0.0000447 AC: 2 AN: 44712

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26122

East Asian (EAS) AF: 0.00 AC: 0 AN: 39692

South Asian (SAS) AF: 0.0000116 AC: 1 AN: 86248

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53326

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5760

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1111758

Other (OTH) AF: 0.00 AC: 0 AN: 60372

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 7092

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Apr 08, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.067
DANN	Benign	0.61
PhyloP100		-1.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2305309; hg19: chr16-57691265;