rs17222202

Variant names:

• chrY-14408564-T-A
• rs17222202

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 0.060 (0 hom., 1962 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0599 AC: 1962 AN: 32772 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00965

Gnomad AMI AF: 0.0238

Gnomad AMR AF: 0.00621

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.00319

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0274

Gnomad NFE AF: 0.0909

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0598 AC: 1962 AN: 32833 Hom.: 0 Cov.: 0 AF XY: 0.0598 AC XY: 1962 AN XY: 32833

African (AFR) AF: 0.00959 AC: 81 AN: 8447

American (AMR) AF: 0.00620 AC: 22 AN: 3549

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 58 AN: 754

East Asian (EAS) AF: 0.00319 AC: 4 AN: 1253

South Asian (SAS) AF: 0.304 AC: 440 AN: 1447

European-Finnish (FIN) AF: 0.0352 AC: 114 AN: 3236

Middle Eastern (MID) AF: 0.0278 AC: 2 AN: 72

European-Non Finnish (NFE) AF: 0.0909 AC: 1218 AN: 13398

Other (OTH) AF: 0.0385 AC: 18 AN: 467

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.14
PhyloP100		-0.29

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17222202;

hg19: chrY-16520444;