rs1013832

Variant names:

• chr13-90799903-G-A
• rs1013832

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0252

Gnomad4 SAS AF: 0.0644

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.148

Alfa AF: 0.179 Hom.: 1270

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

Splicing

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

Publications

LitVar

Other links and lift over

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