rs1163830

Variant names:

• chr13-111460733-G-A
• rs1163830

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.500 AC: 20716 AN: 41400

American (AMR) AF: 0.336 AC: 5141 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1461 AN: 3470

East Asian (EAS) AF: 0.185 AC: 953 AN: 5158

South Asian (SAS) AF: 0.303 AC: 1458 AN: 4804

European-Finnish (FIN) AF: 0.405 AC: 4282 AN: 10568

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29294 AN: 67922

Other (OTH) AF: 0.428 AC: 903 AN: 2108

Alfa AF: 0.416 Hom.: 9899

Bravo AF: 0.427

Asia WGS AF: 0.282 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.75
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1163830; hg19: chr13-112113080;