10-94761288-C-T

Variant names:

• chr10-94761288-C-T
• rs3814637
• ENST00000464755.1:n.932-13770C>T

Variant summary

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

The ENST00000464755.1(ENSG00000276490):​n.932-13770C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0802 in 151,838 control chromosomes in the GnomAD database, including 571 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 0.080 (571 hom., cov: 32)
• Consequence: ENSG00000276490 ENST00000464755.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 25 publications found

Genes affected

ENSG00000276490 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.113 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
ENSG00000276490	ENST00000464755.1	n.932-13770C>T		intron_variant	Intron 6 of 13	2		ENSP00000483243.1

Frequencies

GnomAD3 genomes AF: 0.0801 AC: 12151 AN: 151720 Hom.: 565 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0568

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.0998

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0667

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.0802 AC: 12181 AN: 151838 Hom.: 571 Cov.: 32 AF XY: 0.0803 AC XY: 5958 AN XY: 74168

African (AFR) AF: 0.112 AC: 4630 AN: 41404

American (AMR) AF: 0.0566 AC: 863 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0844 AC: 293 AN: 3472

East Asian (EAS) AF: 0.0998 AC: 516 AN: 5170

South Asian (SAS) AF: 0.121 AC: 580 AN: 4792

European-Finnish (FIN) AF: 0.0520 AC: 546 AN: 10496

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0668 AC: 4536 AN: 67952

Other (OTH) AF: 0.0806 AC: 170 AN: 2110

Alfa AF: 0.0589 Hom.: 113

Bravo AF: 0.0800

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.66
PhyloP100		-0.23

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

Other links and lift over

dbSNP: rs3814637; hg19: chr10-96521045;