ENST00000464755.1:n.932-13241T>G

Variant names:

• chr10-94761817-T-G
• rs11568732
• ENST00000464755.1:n.932-13241T>G

Variant summary

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

The ENST00000464755.1(ENSG00000276490):​n.932-13241T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0683 in 152,260 control chromosomes in the GnomAD database, including 413 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 0.068 (413 hom., cov: 32)
• Consequence: ENSG00000276490 ENST00000464755.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 26 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.111 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.932-13241T>G		intron_variant	Intron 6 of 13	2		ENSP00000483243.1

Frequencies

GnomAD3 genomes AF: 0.0683 AC: 10386 AN: 152142 Hom.: 410 Cov.: 32

Gnomad AFR AF: 0.0759

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0523

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.0991

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0511

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0638

Gnomad OTH AF: 0.0678

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

GnomAD4 genome AF: 0.0683 AC: 10392 AN: 152260 Hom.: 413 Cov.: 32 AF XY: 0.0685 AC XY: 5098 AN XY: 74444

African (AFR) AF: 0.0758 AC: 3151 AN: 41552

American (AMR) AF: 0.0521 AC: 798 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3470

East Asian (EAS) AF: 0.0992 AC: 514 AN: 5184

South Asian (SAS) AF: 0.119 AC: 576 AN: 4826

European-Finnish (FIN) AF: 0.0511 AC: 541 AN: 10582

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0638 AC: 4339 AN: 68020

Other (OTH) AF: 0.0699 AC: 148 AN: 2116

Alfa AF: 0.0403 Hom.: 33

Bravo AF: 0.0665

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.46
PhyloP100		-0.27

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: rs11568732; hg19: chr10-96521574;