11-13253006-A-T

Variant names:

• chr11-13253006-A-T
• rs747601
• ENST00000787640.1:n.65+1055A>T

Variant summary

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

The ENST00000787640.1(ENSG00000302524):​n.65+1055A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 151,842 control chromosomes in the GnomAD database, including 33,224 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 0.66 (33224 hom., cov: 31)
• Consequence: ENSG00000302524 ENST00000787640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413
• Publications: 16 publications found

Genes affected

ENSG00000302524 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787640.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302524	ENST00000787640.1		n.65+1055A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99461 AN: 151724 Hom.: 33174 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.656 AC: 99569 AN: 151842 Hom.: 33224 Cov.: 31 AF XY: 0.657 AC XY: 48796 AN XY: 74224

African (AFR) AF: 0.541 AC: 22389 AN: 41348

American (AMR) AF: 0.652 AC: 9952 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2478 AN: 3470

East Asian (EAS) AF: 0.496 AC: 2547 AN: 5134

South Asian (SAS) AF: 0.650 AC: 3127 AN: 4808

European-Finnish (FIN) AF: 0.741 AC: 7834 AN: 10576

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49082 AN: 67930

Other (OTH) AF: 0.676 AC: 1424 AN: 2106

Alfa AF: 0.687 Hom.: 4257

Bravo AF: 0.646

Asia WGS AF: 0.585 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.64
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs747601; hg19: chr11-13274553;