rs2513265

Positions:

• chr11-105553068-T-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;