rs17127526

Variant names:

• chr14-54391243-G-A
• rs17127526

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 0.0692 in 152,160 control chromosomes in the GnomAD database, including 564 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 0.069 (564 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 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: 0.0693 AC: 10543 AN: 152042 Hom.: 566 Cov.: 31

Gnomad AFR AF: 0.0707

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0533

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.0246

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0545

Gnomad OTH AF: 0.0862

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

GnomAD4 genome AF: 0.0692 AC: 10537 AN: 152160 Hom.: 564 Cov.: 31 AF XY: 0.0711 AC XY: 5290 AN XY: 74384

Gnomad4 AFR AF: 0.0707

Gnomad4 AMR AF: 0.0531

Gnomad4 ASJ AF: 0.0657

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.0246

Gnomad4 NFE AF: 0.0545

Gnomad4 OTH AF: 0.0867

Alfa AF: 0.0595 Hom.: 301

Bravo AF: 0.0701

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17127526; hg19: chr14-54857961;