rs9572423

Variant names:

• chr13-70272071-G-A
• rs9572423

Your query was ambiguous. Multiple possible variants found:

• chr13-70272071-G-A
• chr13-70272071-G-C

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 0.151 in 151,734 control chromosomes in the GnomAD database, including 2,236 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 0.15 (2236 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 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: 0.151 AC: 22928 AN: 151614 Hom.: 2219 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.151 AC: 22980 AN: 151734 Hom.: 2236 Cov.: 32 AF XY: 0.158 AC XY: 11711 AN XY: 74184

African (AFR) AF: 0.151 AC: 6246 AN: 41460

American (AMR) AF: 0.248 AC: 3755 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3464

East Asian (EAS) AF: 0.493 AC: 2530 AN: 5130

South Asian (SAS) AF: 0.141 AC: 682 AN: 4820

European-Finnish (FIN) AF: 0.134 AC: 1416 AN: 10602

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7432 AN: 67792

Other (OTH) AF: 0.169 AC: 355 AN: 2098

Alfa AF: 0.137 Hom.: 3834

Bravo AF: 0.166

Asia WGS AF: 0.309 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.68
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs9572423; hg19: chr13-70846203; COSMIC: COSV107152513;