rs11265501

Variant names:

• chr1-160867138-G-A
• rs11265501

Variant summary

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

The variant allele was found at a frequency of 0.318 in 151,990 control chromosomes in the GnomAD database, including 9,702 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 0.32 (9702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 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: 0.318 AC: 48227 AN: 151872 Hom.: 9687 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.318 AC: 48293 AN: 151990 Hom.: 9702 Cov.: 32 AF XY: 0.318 AC XY: 23637 AN XY: 74288

African (AFR) AF: 0.572 AC: 23694 AN: 41424

American (AMR) AF: 0.255 AC: 3891 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1992 AN: 5160

South Asian (SAS) AF: 0.350 AC: 1687 AN: 4816

European-Finnish (FIN) AF: 0.193 AC: 2033 AN: 10560

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13447 AN: 67966

Other (OTH) AF: 0.287 AC: 606 AN: 2110

Alfa AF: 0.271 Hom.: 868

Bravo AF: 0.329

Asia WGS AF: 0.422 AC: 1469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.52
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs11265501; hg19: chr1-160836928;