chr13-111922883-G-A

Position:

• chr13-111922883-G-A

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 0.829 in 152,142 control chromosomes in the GnomAD database, including 54,530 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 0.83 (54530 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.830 AC: 126128 AN: 152024 Hom.: 54519 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.829 AC: 126176 AN: 152142 Hom.: 54530 Cov.: 32 AF XY: 0.832 AC XY: 61867 AN XY: 74374

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.931

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.925

Gnomad4 FIN AF: 0.920

Gnomad4 NFE AF: 0.938

Gnomad4 OTH AF: 0.849

Alfa AF: 0.917 Hom.: 62338

Bravo AF: 0.818

Asia WGS AF: 0.933 AC: 3246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9604365; hg19: chr13-112577197;