rs17256713

Variant names:

• chr14-24170490-C-T
• rs17256713

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 0.0874 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0518 AC: 2151 AN: 41522

American (AMR) AF: 0.0720 AC: 1102 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3470

East Asian (EAS) AF: 0.353 AC: 1829 AN: 5180

South Asian (SAS) AF: 0.0533 AC: 257 AN: 4820

European-Finnish (FIN) AF: 0.146 AC: 1542 AN: 10560

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0896 AC: 6096 AN: 68020

Other (OTH) AF: 0.0822 AC: 174 AN: 2116

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs17256713; hg19: chr14-24639699;