11-13263734-T-G

Variant names:

• chr11-13263734-T-G
• rs2403661
• ENST00000787640.1:n.248+1509T>G

Variant summary

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

The ENST00000787640.1(ENSG00000302524):​n.248+1509T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 151,916 control chromosomes in the GnomAD database, including 35,238 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 0.68 (35238 hom., cov: 31)
• Consequence: ENSG00000302524 ENST00000787640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 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
ENSG00000302524	ENST00000787640.1	n.248+1509T>G		intron_variant	Intron 3 of 3
ENSG00000302524	ENST00000787641.1	n.173+1509T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103205 AN: 151798 Hom.: 35196 Cov.: 31

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.680 AC: 103301 AN: 151916 Hom.: 35238 Cov.: 31 AF XY: 0.681 AC XY: 50548 AN XY: 74250

African (AFR) AF: 0.671 AC: 27788 AN: 41424

American (AMR) AF: 0.638 AC: 9740 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2294 AN: 3468

East Asian (EAS) AF: 0.536 AC: 2768 AN: 5160

South Asian (SAS) AF: 0.639 AC: 3082 AN: 4820

European-Finnish (FIN) AF: 0.724 AC: 7638 AN: 10550

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47802 AN: 67926

Other (OTH) AF: 0.689 AC: 1452 AN: 2106

Alfa AF: 0.687 Hom.: 18818

Bravo AF: 0.676

Asia WGS AF: 0.612 AC: 2129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.8
DANN	Benign	0.71
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs2403661; hg19: chr11-13285281;