13-88110091-C-T

Position:

• chr13-88110091-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;