rs2031836

chr13-109386243-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;