rs1163830

Variant names:

• chr13-111460733-G-A
• rs1163830

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;