rs11586313

Variant names:

• chr1-152917994-G-A
• rs11586313

Your query was ambiguous. Multiple possible variants found:

• chr1-152917994-G-A
• chr1-152917994-G-C
• chr1-152917994-G-T

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 0.515 in 151,634 control chromosomes in the GnomAD database, including 20,097 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 0.51 (20097 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 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: 0.515 AC: 77981 AN: 151516 Hom.: 20080 Cov.: 30

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.515 AC: 78037 AN: 151634 Hom.: 20097 Cov.: 30 AF XY: 0.509 AC XY: 37709 AN XY: 74068

African (AFR) AF: 0.510 AC: 21052 AN: 41308

American (AMR) AF: 0.485 AC: 7384 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1702 AN: 3468

East Asian (EAS) AF: 0.644 AC: 3301 AN: 5122

South Asian (SAS) AF: 0.474 AC: 2273 AN: 4794

European-Finnish (FIN) AF: 0.415 AC: 4355 AN: 10498

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36310 AN: 67920

Other (OTH) AF: 0.502 AC: 1057 AN: 2104

Alfa AF: 0.510 Hom.: 16757

Bravo AF: 0.522

Asia WGS AF: 0.512 AC: 1783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.1
DANN	Benign	0.89
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs11586313; hg19: chr1-152890470;