1-23225130-A-C

Variant names:

• chr1-23225130-A-C
• rs7532266

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 0.663 in 151,990 control chromosomes in the GnomAD database, including 33,715 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 0.66 (33715 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100674 AN: 151872 Hom.: 33687 Cov.: 31

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.663 AC: 100744 AN: 151990 Hom.: 33715 Cov.: 31 AF XY: 0.666 AC XY: 49470 AN XY: 74288

African (AFR) AF: 0.567 AC: 23456 AN: 41400

American (AMR) AF: 0.737 AC: 11262 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2170 AN: 3472

East Asian (EAS) AF: 0.727 AC: 3748 AN: 5152

South Asian (SAS) AF: 0.735 AC: 3539 AN: 4816

European-Finnish (FIN) AF: 0.679 AC: 7189 AN: 10588

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47012 AN: 67972

Other (OTH) AF: 0.676 AC: 1427 AN: 2112

Alfa AF: 0.678 Hom.: 15944

Bravo AF: 0.662

Asia WGS AF: 0.729 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.40
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs7532266; hg19: chr1-23551623;