rs747931

Variant names:

• chr13-20126789-A-G
• rs747931

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 0.297 in 152,000 control chromosomes in the GnomAD database, including 7,644 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 0.30 (7644 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

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 = 0.386 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: 0.297 AC: 45128 AN: 151882 Hom.: 7649 Cov.: 30

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.297 AC: 45126 AN: 152000 Hom.: 7644 Cov.: 30 AF XY: 0.292 AC XY: 21676 AN XY: 74272

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.325

Alfa AF: 0.376 Hom.: 10914

Bravo AF: 0.283

Asia WGS AF: 0.250 AC: 871 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	1.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs747931; hg19: chr13-20700928;