rs12517663

Variant names:

• chr5-172795342-C-T
• rs12517663

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 0.38 in 151,886 control chromosomes in the GnomAD database, including 11,604 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 0.38 (11604 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57698 AN: 151768 Hom.: 11601 Cov.: 31

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.380 AC: 57712 AN: 151886 Hom.: 11604 Cov.: 31 AF XY: 0.378 AC XY: 28075 AN XY: 74226

African (AFR) AF: 0.250 AC: 10359 AN: 41400

American (AMR) AF: 0.454 AC: 6934 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1575 AN: 3470

East Asian (EAS) AF: 0.239 AC: 1232 AN: 5164

South Asian (SAS) AF: 0.291 AC: 1404 AN: 4818

European-Finnish (FIN) AF: 0.467 AC: 4924 AN: 10538

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29880 AN: 67926

Other (OTH) AF: 0.385 AC: 810 AN: 2106

Alfa AF: 0.408 Hom.: 11158

Bravo AF: 0.377

Asia WGS AF: 0.269 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.65
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs12517663; hg19: chr5-172222345; COSMIC: COSV60231740;