chr6-142302089-G-A

Position:

• chr6-142302089-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_198569.3(ADGRG6):​c.-241G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 530,788 control chromosomes in the GnomAD database, including 1,637 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.072 (1301 hom., cov: 32)
  • Exomes 𝑓: 0.0092 (336 hom.)
• Consequence: ADGRG6 NM_198569.3 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.38

Genes affected

ADGRG6 (HGNC:13841): (adhesion G protein-coupled receptor G6) This gene, which is upregulated in human umbilical vein endothelial cells, encodes a G protein-coupled receptor. Variations in this gene can affect a person's stature. Multiple transcript variants encoding different proteins have been found for this gene. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 6-142302089-G-A is Benign according to our data. Variant chr6-142302089-G-A is described in ClinVar as [Benign]. Clinvar id is 1277642.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRG6	NM_198569.3	c.-241G>A		5_prime_UTR_variant	1/25	ENST00000367609.8	NP_940971.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRG6	ENST00000367609.8	c.-241G>A		5_prime_UTR_variant	1/25	1	NM_198569.3	ENSP00000356581

Frequencies

GnomAD3 genomes AF: 0.0718 AC: 10915 AN: 152072 Hom.: 1291 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0275

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00165

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.000882

Gnomad OTH AF: 0.0609

GnomAD4 exome AF: 0.00921 AC: 3485 AN: 378598 Hom.: 336 Cov.: 3 AF XY: 0.00789 AC XY: 1566 AN XY: 198424

Gnomad4 AFR exome AF: 0.245

Gnomad4 AMR exome AF: 0.0160

Gnomad4 ASJ exome AF: 0.0126

Gnomad4 EAS exome AF: 0.000112

Gnomad4 SAS exome AF: 0.000538

Gnomad4 FIN exome AF: 0.0000347

Gnomad4 NFE exome AF: 0.000836

Gnomad4 OTH exome AF: 0.0227

GnomAD4 genome AF: 0.0720 AC: 10953 AN: 152190 Hom.: 1301 Cov.: 32 AF XY: 0.0695 AC XY: 5174 AN XY: 74428

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.0274

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000882

Gnomad4 OTH AF: 0.0602

Alfa AF: 0.0551 Hom.: 93

Bravo AF: 0.0828

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 25, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.87

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

Publications

LitVar

Other links and lift over

dbSNP: rs112490548; hg19: chr6-142623226;