rs9389983

chr6-142312607-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198569.3(ADGRG6):c.103+2963T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 151,910 control chromosomes in the GnomAD database, including 34,078 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.64 (34078 hom., cov: 32)
• Consequence: ADGRG6 NM_198569.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADGRG6	NM_198569.3	c.103+2963T>C		intron_variant		ENST00000367609.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADGRG6	ENST00000367609.8	c.103+2963T>C		intron_variant		1	NM_198569.3

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97826 AN: 151792 Hom.: 34017 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.651

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.645 AC: 97941 AN: 151910 Hom.: 34078 Cov.: 32 AF XY: 0.644 AC XY: 47817 AN XY: 74230

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.651

Alfa AF: 0.539 Hom.: 28388

Bravo AF: 0.665

Asia WGS AF: 0.718 AC: 2494 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.046
Dann	Benign	0.41

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: rs9389983; hg19: chr6-142633744;