6-142349725-C-A

Position:

• chr6-142349725-C-A

Variant summary

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

The NM_198569.3(ADGRG6):​c.104-17844C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,648 control chromosomes in the GnomAD database, including 11,098 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 0.37 (11098 hom., cov: 31)
• Consequence: ADGRG6 NM_198569.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADGRG6	NM_198569.3	c.104-17844C>A		intron_variant		ENST00000367609.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADGRG6	ENST00000367609.8	c.104-17844C>A		intron_variant		1	NM_198569.3

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55531 AN: 151534 Hom.: 11068 Cov.: 31

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.367 AC: 55616 AN: 151648 Hom.: 11098 Cov.: 31 AF XY: 0.366 AC XY: 27129 AN XY: 74062

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.377

Alfa AF: 0.223 Hom.: 672

Bravo AF: 0.377

Asia WGS AF: 0.393 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.0
DANN	Benign	0.22

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: rs7774095; hg19: chr6-142670862;