rs17315772

chrY-16926422-A-C

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 0.156 in 31,562 control chromosomes in the GnomAD database, with no homozygous occurrence. 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;