rs2031836

Variant names:

• chr13-109386243-G-A
• rs2031836

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 0.381 in 152,080 control chromosomes in the GnomAD database, including 12,052 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 0.38 (12052 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 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: 0.381 AC: 57871 AN: 151964 Hom.: 12049 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.381 AC: 57892 AN: 152080 Hom.: 12052 Cov.: 33 AF XY: 0.378 AC XY: 28098 AN XY: 74336

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.384

Alfa AF: 0.455 Hom.: 32709

Bravo AF: 0.374

Asia WGS AF: 0.356 AC: 1238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2031836; hg19: chr13-110038590;