chr6-126976288-T-C

Variant names:

• chr6-126976288-T-C
• rs988693
• ENST00000650648.1:n.477-32680A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650648.1(ENSG00000293110):​n.477-32680A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,958 control chromosomes in the GnomAD database, including 17,273 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 0.47 (17273 hom., cov: 32)
• Consequence: ENSG00000293110 ENST00000650648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 5 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377989	XR_002956387.2	n.3715+23995A>G		intron_variant	Intron 7 of 13
LOC105377989	XR_007059743.1	n.879+23995A>G		intron_variant	Intron 6 of 8
LOC105377989	XR_007059744.1	n.879+23995A>G		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293110	ENST00000650648.1	n.477-32680A>G		intron_variant	Intron 4 of 7
ENSG00000293110	ENST00000650684.1	n.863+23995A>G		intron_variant	Intron 6 of 8
ENSG00000293110	ENST00000650727.1	n.729+27897A>G		intron_variant	Intron 5 of 14

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72086 AN: 151838 Hom.: 17255 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.475 AC: 72148 AN: 151958 Hom.: 17273 Cov.: 32 AF XY: 0.476 AC XY: 35366 AN XY: 74270

African (AFR) AF: 0.508 AC: 21037 AN: 41448

American (AMR) AF: 0.423 AC: 6458 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1758 AN: 3460

East Asian (EAS) AF: 0.690 AC: 3555 AN: 5152

South Asian (SAS) AF: 0.444 AC: 2137 AN: 4808

European-Finnish (FIN) AF: 0.451 AC: 4761 AN: 10560

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30837 AN: 67954

Other (OTH) AF: 0.462 AC: 974 AN: 2108

Alfa AF: 0.454 Hom.: 3185

Bravo AF: 0.478

Asia WGS AF: 0.501 AC: 1742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.059
DANN	Benign	0.59
PhyloP100		-0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs988693; hg19: chr6-127297433; COSMIC: COSV69425851;