rs17252296

Variant names:

• chr14-51114203-A-C
• rs17252296

Your query was ambiguous. Multiple possible variants found:

• chr14-51114203-A-C
• chr14-51114203-A-G
• chr14-51114203-A-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 0.2 in 151,964 control chromosomes in the GnomAD database, including 3,353 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 0.20 (3353 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812

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 (NFE) allele frequency at 95% confidence interval = 0.245 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: 0.200 AC: 30349 AN: 151846 Hom.: 3352 Cov.: 31

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.0423

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.200 AC: 30365 AN: 151964 Hom.: 3353 Cov.: 31 AF XY: 0.198 AC XY: 14699 AN XY: 74266

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.0422

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.202

Alfa AF: 0.139 Hom.: 336

Bravo AF: 0.192

Asia WGS AF: 0.113 AC: 394 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	1.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17252296; hg19: chr14-51580921;