rs11591064

chr1-40926546-C-Achr1-40926546-C-Gchr1-40926546-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;