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. The variant received -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
• 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 (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

African (AFR) AF: 0.250 AC: 10381 AN: 41466

American (AMR) AF: 0.0972 AC: 1477 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.0880 AC: 305 AN: 3464

East Asian (EAS) AF: 0.285 AC: 1468 AN: 5146

South Asian (SAS) AF: 0.180 AC: 866 AN: 4824

European-Finnish (FIN) AF: 0.0736 AC: 780 AN: 10596

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.0637 AC: 4323 AN: 67884

Other (OTH) AF: 0.135 AC: 285 AN: 2108

Alfa AF: 0.0785 Hom.: 613

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
PhyloP100		0.031

Splicing

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

Other links and lift over

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