rs17250114

Positions:

• chrY-18672817-C-G

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 0.070 (0 hom., 2331 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 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: 0.0705 AC: 2331 AN: 33045 Hom.: 0 Cov.: 0 AF XY: 0.0705 AC XY: 2331 AN XY: 33045

Gnomad AFR AF: 0.0260

Gnomad AMI AF: 0.0282

Gnomad AMR AF: 0.0225

Gnomad ASJ AF: 0.00262

Gnomad EAS AF: 0.000794

Gnomad SAS AF: 0.000690

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0519

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

GnomAD4 genome AF: 0.0704 AC: 2331 AN: 33108 Hom.: 0 Cov.: 0 AF XY: 0.0704 AC XY: 2331 AN XY: 33108

Gnomad4 AFR AF: 0.0258

Gnomad4 AMR AF: 0.0225

Gnomad4 ASJ AF: 0.00262

Gnomad4 EAS AF: 0.000795

Gnomad4 SAS AF: 0.000689

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0515

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17250114; hg19: chrY-20834703;