13-88110091-C-T

Variant names:

• chr13-88110091-C-T
• rs969962

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.879

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.869

Alfa AF: 0.838 Hom.: 110682

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs969962; hg19: chr13-88762346;