rs17315835

Variant names:

• chrY-17067455-T-C
• rs17315835

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.049 (0 hom., 1624 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 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: 0.0489 AC: 1623 AN: 33222 Hom.: 0 Cov.: 0 AF XY: 0.0489 AC XY: 1623 AN XY: 33222

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0798

Gnomad AMR AF: 0.0806

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.000797

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.000904

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.0483

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.0488 AC: 1624 AN: 33287 Hom.: 0 Cov.: 0 AF XY: 0.0488 AC XY: 1624 AN XY: 33287

Gnomad4 AFR AF: 0.0107

Gnomad4 AMR AF: 0.0804

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.000797

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.000904

Gnomad4 NFE AF: 0.0484

Gnomad4 OTH AF: 0.130

Alfa AF: 0.383 Hom.: 404

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.2
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17315835; hg19: chrY-19179335;