chr1-22940446-G-A

Variant names:

• chr1-22940446-G-A
• rs1832047

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 0.0827 in 151,998 control chromosomes in the GnomAD database, including 728 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 0.083 (728 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0828 AC: 12573 AN: 151880 Hom.: 728 Cov.: 31

Gnomad AFR AF: 0.0220

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0680

Gnomad ASJ AF: 0.0944

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0414

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0875

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

GnomAD4 genome AF: 0.0827 AC: 12569 AN: 151998 Hom.: 728 Cov.: 31 AF XY: 0.0824 AC XY: 6119 AN XY: 74304

African (AFR) AF: 0.0220 AC: 910 AN: 41448

American (AMR) AF: 0.0679 AC: 1036 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0944 AC: 327 AN: 3464

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.0417 AC: 201 AN: 4822

European-Finnish (FIN) AF: 0.152 AC: 1598 AN: 10532

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8148 AN: 67980

Other (OTH) AF: 0.0866 AC: 183 AN: 2114

Alfa AF: 0.0775 Hom.: 129

Bravo AF: 0.0726

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.78
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1832047; hg19: chr1-23266939;