6-127114919-C-T

Variant names:

• chr6-127114919-C-T
• rs1936800
• ENST00000650648.1:n.402-43833G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000650648.1(ENSG00000293110):​n.402-43833G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 152,074 control chromosomes in the GnomAD database, including 19,937 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 0.51 (19937 hom., cov: 33)
• Consequence: ENSG00000293110 ENST00000650648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 64 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377989	XR_002956387.2	n.3325+3982G>A		intron_variant	Intron 4 of 13
LOC105377989	XR_007059743.1	n.490-43833G>A		intron_variant	Intron 3 of 8
LOC105377989	XR_007059744.1	n.490-43833G>A		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293110	ENST00000650648.1	n.402-43833G>A		intron_variant	Intron 3 of 7
ENSG00000293110	ENST00000650684.1	n.474-43833G>A		intron_variant	Intron 3 of 8
ENSG00000293110	ENST00000650727.1	n.441-43833G>A		intron_variant	Intron 3 of 14

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77826 AN: 151954 Hom.: 19920 Cov.: 33

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.512 AC: 77892 AN: 152074 Hom.: 19937 Cov.: 33 AF XY: 0.508 AC XY: 37756 AN XY: 74328

African (AFR) AF: 0.540 AC: 22404 AN: 41478

American (AMR) AF: 0.476 AC: 7279 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1558 AN: 3466

East Asian (EAS) AF: 0.522 AC: 2700 AN: 5170

South Asian (SAS) AF: 0.497 AC: 2394 AN: 4814

European-Finnish (FIN) AF: 0.461 AC: 4874 AN: 10568

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35156 AN: 67976

Other (OTH) AF: 0.485 AC: 1024 AN: 2112

Alfa AF: 0.517 Hom.: 28792

Bravo AF: 0.514

Asia WGS AF: 0.520 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	16
DANN	Benign	0.65
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1936800; hg19: chr6-127436064; COSMIC: COSV63150114;