chr13-55267803-C-T

Variant names:

• chr13-55267803-C-T
• rs1370072

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 0.34 in 151,920 control chromosomes in the GnomAD database, including 10,549 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 (10549 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• 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: 51721 AN: 151802 Hom.: 10551 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.340 AC: 51718 AN: 151920 Hom.: 10549 Cov.: 32 AF XY: 0.342 AC XY: 25382 AN XY: 74226

African (AFR) AF: 0.121 AC: 5012 AN: 41494

American (AMR) AF: 0.375 AC: 5710 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1430 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1364 AN: 5138

South Asian (SAS) AF: 0.267 AC: 1289 AN: 4824

European-Finnish (FIN) AF: 0.521 AC: 5499 AN: 10548

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30288 AN: 67930

Other (OTH) AF: 0.349 AC: 735 AN: 2104

Alfa AF: 0.408 Hom.: 11367

Bravo AF: 0.322

Asia WGS AF: 0.246 AC: 855 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	15
DANN	Benign	0.63
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1370072; hg19: chr13-55841938; COSMIC: COSV69351540;