6-126530014-C-T

Variant names:

• chr6-126530014-C-T
• rs1490384
• ENST00000650727.1:n.3036+1649G>A

Variant summary

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

The ENST00000650727.1(ENSG00000293110):​n.3036+1649G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,768 control chromosomes in the GnomAD database, including 18,487 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 0.46 (18487 hom., cov: 31)
• Consequence: ENSG00000293110 ENST00000650727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.25
• Publications: 80 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=-0.23).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293110	ENST00000650727.1	n.3036+1649G>A		intron_variant	Intron 14 of 14
ENSG00000293110	ENST00000651326.1	n.2289+43758G>A		intron_variant	Intron 5 of 6
ENSG00000293110	ENST00000652383.1	n.630+1649G>A		intron_variant	Intron 3 of 4
ENSG00000293110	ENST00000652545.1	n.3346+1649G>A		intron_variant	Intron 15 of 15

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69406 AN: 151650 Hom.: 18485 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.457 AC: 69409 AN: 151768 Hom.: 18487 Cov.: 31 AF XY: 0.467 AC XY: 34659 AN XY: 74140

African (AFR) AF: 0.209 AC: 8657 AN: 41438

American (AMR) AF: 0.632 AC: 9621 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1953 AN: 3466

East Asian (EAS) AF: 0.973 AC: 4973 AN: 5110

South Asian (SAS) AF: 0.715 AC: 3439 AN: 4812

European-Finnish (FIN) AF: 0.472 AC: 4959 AN: 10506

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.503 AC: 34120 AN: 67896

Other (OTH) AF: 0.492 AC: 1037 AN: 2108

Alfa AF: 0.505 Hom.: 60964

Bravo AF: 0.461

Asia WGS AF: 0.706 AC: 2452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	17
DANN	Benign	0.65
PhyloP100		3.3

Splicing

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

Other links and lift over

dbSNP: rs1490384; hg19: chr6-126851160; COSMIC: COSV69424814;