rs11162922

Variant names:

• chr1-80106373-A-G
• rs11162922

Your query was ambiguous. Multiple possible variants found:

• chr1-80106373-A-G
• chr1-80106373-A-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 0.132 in 151,890 control chromosomes in the GnomAD database, including 1,913 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 0.13 (1913 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 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: 0.132 AC: 20040 AN: 151774 Hom.: 1906 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.0880

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0636

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.132 AC: 20089 AN: 151890 Hom.: 1913 Cov.: 32 AF XY: 0.135 AC XY: 10041 AN XY: 74250

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.0972

Gnomad4 ASJ AF: 0.0880

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.0736

Gnomad4 NFE AF: 0.0637

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0752 Hom.: 468

Bravo AF: 0.139

Asia WGS AF: 0.242 AC: 833 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11162922; hg19: chr1-80572058; COSMIC: COSV59961964;