rs11591064

Variant names:

• chr1-40926546-C-A
• rs11591064

Your query was ambiguous. Multiple possible variants found:

• chr1-40926546-C-A
• chr1-40926546-C-G
• chr1-40926546-C-T

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 0.107 in 152,020 control chromosomes in the GnomAD database, including 985 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 0.11 (985 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 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: 0.108 AC: 16345 AN: 151904 Hom.: 987 Cov.: 31

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0920

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.107 AC: 16338 AN: 152020 Hom.: 985 Cov.: 31 AF XY: 0.104 AC XY: 7748 AN XY: 74324

Gnomad4 AFR AF: 0.0681

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0927

Gnomad4 FIN AF: 0.0925

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0532 Hom.: 68

Bravo AF: 0.107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.56
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11591064; hg19: chr1-41392218; COSMIC: COSV59940700;