13-55410861-C-T

Variant names:

• chr13-55410861-C-T
• rs2315885

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 0.212 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0546 AC: 2267 AN: 41532

American (AMR) AF: 0.187 AC: 2857 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1113 AN: 3470

East Asian (EAS) AF: 0.00330 AC: 17 AN: 5158

South Asian (SAS) AF: 0.152 AC: 732 AN: 4824

European-Finnish (FIN) AF: 0.303 AC: 3200 AN: 10576

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21313 AN: 68000

Other (OTH) AF: 0.237 AC: 500 AN: 2114

Alfa AF: 0.205 Hom.: 1197

Bravo AF: 0.198

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.50
PhyloP100		-2.3

Splicing

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

Other links and lift over

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