Y-15174113-T-C

Variant names:

• chrY-15174113-T-C
• rs17307398

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.59 (0 hom., 18748 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 7 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

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: 0.584 AC: 18679 AN: 31986 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.958

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.581

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.585 AC: 18748 AN: 32047 Hom.: 0 Cov.: 0 AF XY: 0.585 AC XY: 18748 AN XY: 32047

African (AFR) AF: 0.791 AC: 6426 AN: 8119

American (AMR) AF: 0.499 AC: 1764 AN: 3538

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 602 AN: 747

East Asian (EAS) AF: 0.996 AC: 1197 AN: 1202

South Asian (SAS) AF: 0.534 AC: 741 AN: 1387

European-Finnish (FIN) AF: 0.932 AC: 2825 AN: 3032

Middle Eastern (MID) AF: 0.957 AC: 66 AN: 69

European-Non Finnish (NFE) AF: 0.362 AC: 4805 AN: 13286

Other (OTH) AF: 0.589 AC: 269 AN: 457

Alfa AF: 0.439 Hom.: 24622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.30
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs17307398; hg19: chrY-17285993;