chrY-19617112-C-G

Variant names:

• chrY-19617112-C-G
• rs9306841

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.210 AC: 6862 AN: 32677 Hom.: 0 Cov.: 0

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

African (AFR) AF: 0.679 AC: 5532 AN: 8150

American (AMR) AF: 0.130 AC: 464 AN: 3573

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 185 AN: 765

East Asian (EAS) AF: 0.00 AC: 0 AN: 1222

South Asian (SAS) AF: 0.00605 AC: 9 AN: 1488

European-Finnish (FIN) AF: 0.00146 AC: 5 AN: 3415

Middle Eastern (MID) AF: 0.324 AC: 22 AN: 68

European-Non Finnish (NFE) AF: 0.0454 AC: 607 AN: 13383

Other (OTH) AF: 0.156 AC: 72 AN: 462

Alfa AF: 0.0650 Hom.: 811

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.4
DANN	Benign	0.38
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs9306841; hg19: chrY-21778998;