rs9572903

Variant names:

• chr13-72197576-A-G
• rs9572903

Your query was ambiguous. Multiple possible variants found:

• chr13-72197576-A-G
• chr13-72197576-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.251 in 151,962 control chromosomes in the GnomAD database, including 5,940 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 0.25 (5940 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.76
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 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: 0.251 AC: 38112 AN: 151844 Hom.: 5931 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.251 AC: 38144 AN: 151962 Hom.: 5940 Cov.: 32 AF XY: 0.258 AC XY: 19183 AN XY: 74280

African (AFR) AF: 0.342 AC: 14169 AN: 41468

American (AMR) AF: 0.331 AC: 5039 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3470

East Asian (EAS) AF: 0.678 AC: 3476 AN: 5128

South Asian (SAS) AF: 0.244 AC: 1176 AN: 4822

European-Finnish (FIN) AF: 0.200 AC: 2110 AN: 10566

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10874 AN: 67962

Other (OTH) AF: 0.254 AC: 535 AN: 2108

Alfa AF: 0.195 Hom.: 5407

Bravo AF: 0.272

Asia WGS AF: 0.386 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Uncertain	23
DANN	Benign	0.80
PhyloP100		6.8

Splicing

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

Other links and lift over

dbSNP: rs9572903; hg19: chr13-72771714;