13-111569284-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 0.85 in 152,242 control chromosomes in the GnomAD database, including 55,403 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 0.85 (55403 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 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: 0.850 AC: 129348 AN: 152124 Hom.: 55376 Cov.: 33

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.850 AC: 129429 AN: 152242 Hom.: 55403 Cov.: 33 AF XY: 0.856 AC XY: 63721 AN XY: 74428

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.901

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.935

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.862

Alfa AF: 0.858 Hom.: 9755

Bravo AF: 0.843

Asia WGS AF: 0.918 AC: 3193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	6.6
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1163623; hg19: chr13-112221631;