rs12517663

Positions:

• chr5-172795342-C-T

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 0.38 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.385

Alfa AF: 0.412 Hom.: 8492

Bravo AF: 0.377

Asia WGS AF: 0.269 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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