6-142421522-T-C

Position:

• chr6-142421522-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_198569.3(ADGRG6):​c.3319+1418T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,036 control chromosomes in the GnomAD database, including 13,586 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 (13586 hom., cov: 32)
• Consequence: ADGRG6 NM_198569.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

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]

ADGRG6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRG6	NM_198569.3	c.3319+1418T>C		intron_variant		ENST00000367609.8	NP_940971.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRG6	ENST00000367609.8	c.3319+1418T>C		intron_variant		1	NM_198569.3	ENSP00000356581.3

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60122 AN: 151918 Hom.: 13555 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.396 AC: 60212 AN: 152036 Hom.: 13586 Cov.: 32 AF XY: 0.393 AC XY: 29205 AN XY: 74318

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.421

Alfa AF: 0.347 Hom.: 3353

Bravo AF: 0.410

Asia WGS AF: 0.434 AC: 1506 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	17
DANN	Benign	0.81

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: rs6929442; hg19: chr6-142742659;