rs641385

Variant names:

• chr13-55298890-A-C
• rs641385

Your query was ambiguous. Multiple possible variants found:

• chr13-55298890-A-C
• chr13-55298890-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 0.341 in 151,926 control chromosomes in the GnomAD database, including 10,555 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 0.34 (10555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

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 = 0.442 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: 0.341 AC: 51750 AN: 151806 Hom.: 10557 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.341 AC: 51747 AN: 151926 Hom.: 10555 Cov.: 32 AF XY: 0.342 AC XY: 25407 AN XY: 74232

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.350

Alfa AF: 0.425 Hom.: 14924

Bravo AF: 0.322

Asia WGS AF: 0.247 AC: 857 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs641385; hg19: chr13-55873025; COSMIC: COSV69351564;