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. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.121 AC: 5001 AN: 41474

American (AMR) AF: 0.376 AC: 5726 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1431 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1374 AN: 5154

South Asian (SAS) AF: 0.268 AC: 1292 AN: 4826

European-Finnish (FIN) AF: 0.523 AC: 5505 AN: 10534

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.446 AC: 30293 AN: 67928

Other (OTH) AF: 0.350 AC: 736 AN: 2100

Alfa AF: 0.411 Hom.: 18373

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
PhyloP100		0.12

Splicing

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

Other links and lift over

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