chr6-142302016-T-G

Position:

• chr6-142302016-T-G

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.-314T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.03 in 468,606 control chromosomes in the GnomAD database, including 1,612 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.073 (1333 hom., cov: 32)
  • Exomes 𝑓: 0.0094 (279 hom.)
• Consequence: ADGRG6 NM_198569.3 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.93

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 6-142302016-T-G is Benign according to our data. Variant chr6-142302016-T-G is described in ClinVar as [Benign]. Clinvar id is 1231718.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRG6	NM_198569.3	c.-314T>G		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.-314T>G		5_prime_UTR_variant	1/25	1	NM_198569.3	ENSP00000356581

Frequencies

GnomAD3 genomes AF: 0.0725 AC: 11029 AN: 152068 Hom.: 1322 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0278

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.000912

Gnomad OTH AF: 0.0608

GnomAD4 exome AF: 0.00945 AC: 2989 AN: 316422 Hom.: 279 Cov.: 0 AF XY: 0.00814 AC XY: 1336 AN XY: 164094

Gnomad4 AFR exome AF: 0.247

Gnomad4 AMR exome AF: 0.0169

Gnomad4 ASJ exome AF: 0.0124

Gnomad4 EAS exome AF: 0.000126

Gnomad4 SAS exome AF: 0.000661

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000945

Gnomad4 OTH exome AF: 0.0237

GnomAD4 genome AF: 0.0727 AC: 11069 AN: 152184 Hom.: 1333 Cov.: 32 AF XY: 0.0702 AC XY: 5224 AN XY: 74400

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.0277

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000912

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0431 Hom.: 93

Bravo AF: 0.0835

Asia WGS AF: 0.0180 AC: 63 AN: 3478

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	0.56
DANN	Benign	0.61

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: rs73576330; hg19: chr6-142623153;