rs2513265

Variant names:

• chr11-105553068-T-A
• rs2513265

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.467 in 151,950 control chromosomes in the GnomAD database, including 16,998 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 0.47 (16998 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 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

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70976 AN: 151832 Hom.: 16989 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.467 AC: 71025 AN: 151950 Hom.: 16998 Cov.: 32 AF XY: 0.463 AC XY: 34422 AN XY: 74270

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.447

Alfa AF: 0.493 Hom.: 2312

Bravo AF: 0.460

Asia WGS AF: 0.380 AC: 1322 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	0.86
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2513265; hg19: chr11-105423795;