chr6-142302510-A-G

Position:

• chr6-142302510-A-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.2+179A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0128 in 590,660 control chromosomes in the GnomAD database, including 148 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.022 (84 hom., cov: 32)
  • Exomes 𝑓: 0.0094 (64 hom.)
• Consequence: ADGRG6 NM_198569.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.01

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=-0.87).
• BP6: Variant 6-142302510-A-G is Benign according to our data. Variant chr6-142302510-A-G is described in ClinVar as [Benign]. Clinvar id is 1270572.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRG6	NM_198569.3	c.2+179A>G		intron_variant		ENST00000367609.8	NP_940971.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRG6	ENST00000367609.8	c.2+179A>G		intron_variant		1	NM_198569.3	ENSP00000356581

Frequencies

GnomAD3 genomes AF: 0.0224 AC: 3410 AN: 152098 Hom.: 84 Cov.: 32

Gnomad AFR AF: 0.0583

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0164

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.000660

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.00650

Gnomad OTH AF: 0.0297

GnomAD4 exome AF: 0.00942 AC: 4131 AN: 438444 Hom.: 64 Cov.: 6 AF XY: 0.00999 AC XY: 2287 AN XY: 228948

Gnomad4 AFR exome AF: 0.0542

Gnomad4 AMR exome AF: 0.0130

Gnomad4 ASJ exome AF: 0.0208

Gnomad4 EAS exome AF: 0.0000723

Gnomad4 SAS exome AF: 0.0224

Gnomad4 FIN exome AF: 0.000777

Gnomad4 NFE exome AF: 0.00634

Gnomad4 OTH exome AF: 0.0151

GnomAD4 genome AF: 0.0224 AC: 3416 AN: 152216 Hom.: 84 Cov.: 32 AF XY: 0.0225 AC XY: 1676 AN XY: 74404

Gnomad4 AFR AF: 0.0583

Gnomad4 AMR AF: 0.0164

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0298

Gnomad4 FIN AF: 0.000660

Gnomad4 NFE AF: 0.00648

Gnomad4 OTH AF: 0.0294

Alfa AF: 0.0124 Hom.: 11

Bravo AF: 0.0249

Asia WGS AF: 0.0120 AC: 43 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 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.042
DANN	Benign	0.30

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: rs115240560; hg19: chr6-142623647;