13-109744675-T-C

Position:

• chr13-109744675-T-C

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 0.575 in 152,060 control chromosomes in the GnomAD database, including 25,480 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 0.58 (25480 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87427 AN: 151940 Hom.: 25469 Cov.: 33

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.575 AC: 87475 AN: 152060 Hom.: 25480 Cov.: 33 AF XY: 0.577 AC XY: 42876 AN XY: 74308

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.581

Alfa AF: 0.605 Hom.: 28069

Bravo AF: 0.579

Asia WGS AF: 0.536 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.028
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1556223; hg19: chr13-110397022;