rs13097326

Variant names:

• chr3-148750959-G-A
• rs13097326

Your query was ambiguous. Multiple possible variants found:

• chr3-148750959-G-A
• chr3-148750959-G-C
• chr3-148750959-G-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 0.195 in 151,980 control chromosomes in the GnomAD database, including 3,724 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 0.19 (3724 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) 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: 0.195 AC: 29557 AN: 151862 Hom.: 3723 Cov.: 30

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0590

Gnomad SAS AF: 0.0774

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.195 AC: 29562 AN: 151980 Hom.: 3724 Cov.: 30 AF XY: 0.188 AC XY: 13967 AN XY: 74306

African (AFR) AF: 0.0608 AC: 2520 AN: 41474

American (AMR) AF: 0.255 AC: 3890 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3470

East Asian (EAS) AF: 0.0594 AC: 307 AN: 5172

South Asian (SAS) AF: 0.0768 AC: 369 AN: 4802

European-Finnish (FIN) AF: 0.164 AC: 1732 AN: 10566

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18777 AN: 67936

Other (OTH) AF: 0.210 AC: 442 AN: 2100

Alfa AF: 0.251 Hom.: 8535

Bravo AF: 0.201

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.90
DANN	Benign	0.45
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs13097326; hg19: chr3-148468746;