chr13-105517256-T-C

Variant names:

• chr13-105517256-T-C
• rs2012887

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 0.403 in 152,002 control chromosomes in the GnomAD database, including 13,667 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 0.40 (13667 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.512 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: 0.403 AC: 61192 AN: 151884 Hom.: 13653 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.403 AC: 61230 AN: 152002 Hom.: 13667 Cov.: 32 AF XY: 0.406 AC XY: 30129 AN XY: 74298

African (AFR) AF: 0.200 AC: 8282 AN: 41498

American (AMR) AF: 0.521 AC: 7951 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2320 AN: 5170

South Asian (SAS) AF: 0.454 AC: 2184 AN: 4810

European-Finnish (FIN) AF: 0.427 AC: 4496 AN: 10532

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 32996 AN: 67950

Other (OTH) AF: 0.403 AC: 851 AN: 2114

Alfa AF: 0.425 Hom.: 1916

Bravo AF: 0.400

Asia WGS AF: 0.398 AC: 1383 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.42
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2012887; hg19: chr13-106169605;