rs1163932

Variant names:

• chr12-17448674-G-A
• rs1163932

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 0.324 in 151,802 control chromosomes in the GnomAD database, including 8,423 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 0.32 (8423 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 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: 0.324 AC: 49129 AN: 151686 Hom.: 8412 Cov.: 29

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.324 AC: 49177 AN: 151802 Hom.: 8423 Cov.: 29 AF XY: 0.324 AC XY: 24059 AN XY: 74164

African (AFR) AF: 0.444 AC: 18355 AN: 41376

American (AMR) AF: 0.314 AC: 4782 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3466

East Asian (EAS) AF: 0.350 AC: 1794 AN: 5128

South Asian (SAS) AF: 0.353 AC: 1699 AN: 4808

European-Finnish (FIN) AF: 0.264 AC: 2775 AN: 10526

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18378 AN: 67938

Other (OTH) AF: 0.311 AC: 656 AN: 2110

Alfa AF: 0.297 Hom.: 1734

Bravo AF: 0.329

Asia WGS AF: 0.381 AC: 1323 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.1
DANN	Benign	0.34
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1163932; hg19: chr12-17601608;