rs1013832

Variant names:

• chr13-90799903-G-A
• rs1013832

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 0.155 in 151,898 control chromosomes in the GnomAD database, including 2,006 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 0.16 (2006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.19 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: 0.155 AC: 23541 AN: 151780 Hom.: 2006 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0252

Gnomad SAS AF: 0.0629

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.155 AC: 23551 AN: 151898 Hom.: 2006 Cov.: 32 AF XY: 0.150 AC XY: 11144 AN XY: 74248

African (AFR) AF: 0.123 AC: 5087 AN: 41394

American (AMR) AF: 0.153 AC: 2334 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 519 AN: 3472

East Asian (EAS) AF: 0.0252 AC: 130 AN: 5154

South Asian (SAS) AF: 0.0644 AC: 310 AN: 4814

European-Finnish (FIN) AF: 0.150 AC: 1578 AN: 10536

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13065 AN: 67952

Other (OTH) AF: 0.148 AC: 311 AN: 2108

Alfa AF: 0.181 Hom.: 1412

Bravo AF: 0.154

Asia WGS AF: 0.0500 AC: 176 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.24
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1013832; hg19: chr13-91452157; COSMIC: COSV53427671;