rs17222573

Variant names:

• chrY-15779361-A-G
• rs17222573

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 0.058 (0 hom., 1941 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.27 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: 0.0582 AC: 1943 AN: 33410 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00976

Gnomad AMI AF: 0.0185

Gnomad AMR AF: 0.00530

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.00238

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.0341

Gnomad MID AF: 0.0270

Gnomad NFE AF: 0.0895

Gnomad OTH AF: 0.0386

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

GnomAD4 genome AF: 0.0580 AC: 1941 AN: 33474 Hom.: 0 Cov.: 0 AF XY: 0.0580 AC XY: 1941 AN XY: 33474

African (AFR) AF: 0.00970 AC: 84 AN: 8658

American (AMR) AF: 0.00529 AC: 19 AN: 3593

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 59 AN: 767

East Asian (EAS) AF: 0.00239 AC: 3 AN: 1257

South Asian (SAS) AF: 0.293 AC: 421 AN: 1438

European-Finnish (FIN) AF: 0.0341 AC: 118 AN: 3457

Middle Eastern (MID) AF: 0.0274 AC: 2 AN: 73

European-Non Finnish (NFE) AF: 0.0895 AC: 1213 AN: 13546

Other (OTH) AF: 0.0384 AC: 18 AN: 469

Alfa AF: 0.0974 Hom.: 4289

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.80
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs17222573; hg19: chrY-17891241;