rs9306841

Variant names:

• chrY-19617112-C-G
• rs9306841

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 0.21 (0 hom., 6896 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 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: 0.210 AC: 6862 AN: 32677 Hom.: 0 Cov.: 0 AF XY: 0.210 AC XY: 6862 AN XY: 32677

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00607

Gnomad FIN AF: 0.00146

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.211 AC: 6896 AN: 32738 Hom.: 0 Cov.: 0 AF XY: 0.211 AC XY: 6896 AN XY: 32738

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00605

Gnomad4 FIN AF: 0.00146

Gnomad4 NFE AF: 0.0454

Gnomad4 OTH AF: 0.156

Alfa AF: 0.0650 Hom.: 811

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.4
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9306841; hg19: chrY-21778998;