rs13072940

Variant names:

• chr3-36801132-T-A
• rs13072940

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 0.364 in 152,038 control chromosomes in the GnomAD database, including 10,518 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 0.36 (10518 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.384 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: 0.365 AC: 55393 AN: 151918 Hom.: 10522 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.0597

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.364 AC: 55413 AN: 152038 Hom.: 10518 Cov.: 32 AF XY: 0.364 AC XY: 27072 AN XY: 74314

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.0597

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.368

Alfa AF: 0.389 Hom.: 1486

Bravo AF: 0.350

Asia WGS AF: 0.209 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	1.8
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13072940; hg19: chr3-36842623;