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).

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: 0.584 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 v4.3

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;