chr13-26721180-C-T

Variant names:

• chr13-26721180-C-T
• rs1374010

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 0.352 in 152,074 control chromosomes in the GnomAD database, including 9,743 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 0.35 (9743 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53400 AN: 151956 Hom.: 9724 Cov.: 33

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.352 AC: 53471 AN: 152074 Hom.: 9743 Cov.: 33 AF XY: 0.354 AC XY: 26336 AN XY: 74322

African (AFR) AF: 0.451 AC: 18687 AN: 41450

American (AMR) AF: 0.393 AC: 6008 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1090 AN: 5182

South Asian (SAS) AF: 0.408 AC: 1970 AN: 4832

European-Finnish (FIN) AF: 0.347 AC: 3665 AN: 10566

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20066 AN: 67984

Other (OTH) AF: 0.346 AC: 731 AN: 2114

Alfa AF: 0.297 Hom.: 5026

Bravo AF: 0.361

Asia WGS AF: 0.315 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.34
DANN	Benign	0.52
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1374010; hg19: chr13-27295317; COSMIC: COSV69344921;