rs17404727

Variant names:

• chr15-49711886-T-C
• rs17404727

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 0.255 in 152,240 control chromosomes in the GnomAD database, including 5,954 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 0.25 (5954 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.815

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 (NFE) allele frequency at 95% confidence interval = 0.35 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: 0.255 AC: 38791 AN: 152122 Hom.: 5954 Cov.: 33

Gnomad AFR AF: 0.0858

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.255 AC: 38775 AN: 152240 Hom.: 5954 Cov.: 33 AF XY: 0.251 AC XY: 18716 AN XY: 74428

Gnomad4 AFR AF: 0.0856

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.271

Alfa AF: 0.311 Hom.: 2451

Asia WGS AF: 0.183 AC: 638 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	7.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17404727; hg19: chr15-50004083;