13-88654335-T-C

Variant names:

• chr13-88654335-T-C
• rs1571056

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 0.0778 in 152,100 control chromosomes in the GnomAD database, including 699 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 0.078 (699 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.274 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: 0.0778 AC: 11830 AN: 151982 Hom.: 696 Cov.: 33

Gnomad AFR AF: 0.0272

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0763

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.0465

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0837

Gnomad OTH AF: 0.0698

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

GnomAD4 genome AF: 0.0778 AC: 11834 AN: 152100 Hom.: 699 Cov.: 33 AF XY: 0.0811 AC XY: 6033 AN XY: 74350

African (AFR) AF: 0.0271 AC: 1127 AN: 41568

American (AMR) AF: 0.0763 AC: 1164 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0418 AC: 145 AN: 3470

East Asian (EAS) AF: 0.286 AC: 1481 AN: 5174

South Asian (SAS) AF: 0.0466 AC: 225 AN: 4830

European-Finnish (FIN) AF: 0.164 AC: 1733 AN: 10560

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0837 AC: 5686 AN: 67924

Other (OTH) AF: 0.0724 AC: 153 AN: 2114

Alfa AF: 0.0427 Hom.: 47

Bravo AF: 0.0751

Asia WGS AF: 0.133 AC: 458 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.77
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs1571056; hg19: chr13-89306589;