rs1163830

Positions:

• chr13-111460733-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 0.427 in 151,912 control chromosomes in the GnomAD database, including 14,258 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 0.43 (14258 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 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: 0.427 AC: 64763 AN: 151794 Hom.: 14242 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.427 AC: 64811 AN: 151912 Hom.: 14258 Cov.: 31 AF XY: 0.422 AC XY: 31324 AN XY: 74242

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.428

Alfa AF: 0.419 Hom.: 7017

Bravo AF: 0.427

Asia WGS AF: 0.282 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1163830; hg19: chr13-112113080;