rs7741741

Positions:

• chr6-142334664-T-A
• chr6-142334664-T-G

Variant summary

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

The NM_198569.3(ADGRG6):​c.103+25020T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,992 control chromosomes in the GnomAD database, including 14,579 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 0.40 (14579 hom., cov: 32)
• Consequence: ADGRG6 NM_198569.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRG6	NM_198569.3	c.103+25020T>A		intron_variant		ENST00000367609.8	NP_940971.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRG6	ENST00000367609.8	c.103+25020T>A		intron_variant		1	NM_198569.3	ENSP00000356581

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61453 AN: 151874 Hom.: 14542 Cov.: 32

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.405 AC: 61555 AN: 151992 Hom.: 14579 Cov.: 32 AF XY: 0.403 AC XY: 29926 AN XY: 74286

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.412

Alfa AF: 0.344 Hom.: 1265

Bravo AF: 0.420

Asia WGS AF: 0.418 AC: 1452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.47

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: rs7741741; hg19: chr6-142655801;