rs17222146

Variant names:

• chrY-14203273-C-T
• rs17222146

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 0.059 (0 hom., 1903 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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: 0.0589 AC: 1906 AN: 32334 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00978

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.00600

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.00318

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.0342

Gnomad MID AF: 0.0137

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.0360

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

GnomAD4 genome AF: 0.0588 AC: 1903 AN: 32374 Hom.: 0 Cov.: 0 AF XY: 0.0588 AC XY: 1903 AN XY: 32374

African (AFR) AF: 0.00973 AC: 81 AN: 8322

American (AMR) AF: 0.00599 AC: 21 AN: 3508

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 58 AN: 768

East Asian (EAS) AF: 0.00318 AC: 4 AN: 1256

South Asian (SAS) AF: 0.293 AC: 410 AN: 1398

European-Finnish (FIN) AF: 0.0342 AC: 105 AN: 3069

Middle Eastern (MID) AF: 0.0143 AC: 1 AN: 70

European-Non Finnish (NFE) AF: 0.0903 AC: 1203 AN: 13323

Other (OTH) AF: 0.0360 AC: 16 AN: 445

Alfa AF: 0.0902 Hom.: 4621

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.052
DANN	Benign	0.28
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs17222146; hg19: chrY-16315153;