rs17315772

Variant names:

• chrY-16926422-A-C
• rs17315772

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 0.16 (0 hom., 4932 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

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 (NFE) allele frequency at 95% confidence interval = 0.224 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: 0.157 AC: 4935 AN: 31512 Hom.: 0 Cov.: 0 AF XY: 0.157 AC XY: 4935 AN XY: 31512

Gnomad AFR AF: 0.0516

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.00163

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.375

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.156 AC: 4932 AN: 31562 Hom.: 0 Cov.: 0 AF XY: 0.156 AC XY: 4932 AN XY: 31562

Gnomad4 AFR AF: 0.0513

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.00163

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.214

Alfa AF: 0.248 Hom.: 4790

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.9
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17315772; hg19: chrY-19038302;