rs1937387

chr13-82466181-A-Gchr13-82466181-A-T

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 0.328 in 151,116 control chromosomes in the GnomAD database, including 8,463 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 0.33 (8463 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 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: 0.329 AC: 49610 AN: 150998 Hom.: 8464 Cov.: 30

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.328 AC: 49622 AN: 151116 Hom.: 8463 Cov.: 30 AF XY: 0.327 AC XY: 24123 AN XY: 73826

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.380

Alfa AF: 0.355 Hom.: 15647

Bravo AF: 0.343

Asia WGS AF: 0.420 AC: 1460 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.14
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1937387; hg19: chr13-83040316;