rs13132933

Variant names:

• chr4-122089432-T-C
• rs13132933

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 0.218 in 152,004 control chromosomes in the GnomAD database, including 4,629 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 0.22 (4629 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 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: 0.218 AC: 33062 AN: 151886 Hom.: 4631 Cov.: 31

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.218 AC: 33095 AN: 152004 Hom.: 4629 Cov.: 31 AF XY: 0.212 AC XY: 15722 AN XY: 74320

African (AFR) AF: 0.396 AC: 16381 AN: 41376

American (AMR) AF: 0.124 AC: 1896 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 427 AN: 3472

East Asian (EAS) AF: 0.0355 AC: 183 AN: 5160

South Asian (SAS) AF: 0.112 AC: 538 AN: 4824

European-Finnish (FIN) AF: 0.129 AC: 1366 AN: 10604

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11755 AN: 67962

Other (OTH) AF: 0.191 AC: 404 AN: 2114

Alfa AF: 0.182 Hom.: 11133

Bravo AF: 0.224

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.76
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs13132933; hg19: chr4-123010587;