chr13-111577767-T-C

Position:

• chr13-111577767-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 0.583 in 151,836 control chromosomes in the GnomAD database, including 25,967 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 (25967 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 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: 0.583 AC: 88402 AN: 151718 Hom.: 25925 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.583 AC: 88507 AN: 151836 Hom.: 25967 Cov.: 31 AF XY: 0.582 AC XY: 43166 AN XY: 74178

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.564

Alfa AF: 0.559 Hom.: 31847

Bravo AF: 0.582

Asia WGS AF: 0.513 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2774440; hg19: chr13-112230114;