rs17101452

Variant names:

• chr14-74621282-C-A
• rs17101452

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 0.0797 in 152,204 control chromosomes in the GnomAD database, including 814 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 0.080 (814 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 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: 0.0796 AC: 12109 AN: 152086 Hom.: 811 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.0869

Gnomad SAS AF: 0.0572

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0779

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

GnomAD4 genome AF: 0.0797 AC: 12129 AN: 152204 Hom.: 814 Cov.: 33 AF XY: 0.0811 AC XY: 6036 AN XY: 74430

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0700

Gnomad4 EAS AF: 0.0869

Gnomad4 SAS AF: 0.0572

Gnomad4 FIN AF: 0.0200

Gnomad4 NFE AF: 0.0255

Gnomad4 OTH AF: 0.0776

Alfa AF: 0.0448 Hom.: 59

Bravo AF: 0.0896

Asia WGS AF: 0.0710 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17101452; hg19: chr14-75087985;