13-88110091-C-T

Variant names:

• chr13-88110091-C-T
• rs969962

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 0.82 in 152,036 control chromosomes in the GnomAD database, including 51,348 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 0.82 (51348 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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: 0.821 AC: 124670 AN: 151918 Hom.: 51326 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.820 AC: 124735 AN: 152036 Hom.: 51348 Cov.: 32 AF XY: 0.822 AC XY: 61084 AN XY: 74298

African (AFR) AF: 0.753 AC: 31258 AN: 41484

American (AMR) AF: 0.872 AC: 13285 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3049 AN: 3470

East Asian (EAS) AF: 0.927 AC: 4766 AN: 5140

South Asian (SAS) AF: 0.888 AC: 4288 AN: 4830

European-Finnish (FIN) AF: 0.816 AC: 8638 AN: 10580

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56670 AN: 67978

Other (OTH) AF: 0.869 AC: 1834 AN: 2110

Alfa AF: 0.834 Hom.: 233452

Bravo AF: 0.821

Asia WGS AF: 0.919 AC: 3195 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.49
DANN	Benign	0.53
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs969962; hg19: chr13-88762346;