13-55410861-C-T

Variant names:

• chr13-55410861-C-T
• rs2315885

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 0.212 in 152,154 control chromosomes in the GnomAD database, including 4,566 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 0.21 (4566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 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: 0.212 AC: 32247 AN: 152036 Hom.: 4571 Cov.: 32

Gnomad AFR AF: 0.0547

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.00329

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.212 AC: 32227 AN: 152154 Hom.: 4566 Cov.: 32 AF XY: 0.208 AC XY: 15477 AN XY: 74378

Gnomad4 AFR AF: 0.0546

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.00330

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.237

Alfa AF: 0.148 Hom.: 330

Bravo AF: 0.198

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2315885; hg19: chr13-55984996; COSMIC: COSV69351593;