rs17256713

chr14-24170490-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 0.0874 in 152,194 control chromosomes in the GnomAD database, including 870 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 0.087 (870 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 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: 0.0875 AC: 13308 AN: 152076 Hom.: 875 Cov.: 31

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0719

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.0533

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.0821

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

GnomAD4 genome AF: 0.0874 AC: 13308 AN: 152194 Hom.: 870 Cov.: 31 AF XY: 0.0913 AC XY: 6794 AN XY: 74386

Gnomad4 AFR AF: 0.0518

Gnomad4 AMR AF: 0.0720

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.0533

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.0896

Gnomad4 OTH AF: 0.0822

Alfa AF: 0.0807 Hom.: 87

Bravo AF: 0.0817

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.1
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17256713; hg19: chr14-24639699;