rs34173183

Variant names:

• chrY-22259715-T-C
• rs34173183

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 0.99 (0 hom., 31313 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.994 AC: 31247 AN: 31428 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.996

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.996

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.993

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.991

Gnomad OTH AF: 0.998

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: 0.994 AC: 31313 AN: 31494 Hom.: 0 Cov.: 0 AF XY: 0.994 AC XY: 31313 AN XY: 31494

African (AFR) AF: 0.996 AC: 8069 AN: 8099

American (AMR) AF: 0.996 AC: 3381 AN: 3394

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 760 AN: 760

East Asian (EAS) AF: 0.993 AC: 1125 AN: 1133

South Asian (SAS) AF: 1.00 AC: 1296 AN: 1296

European-Finnish (FIN) AF: 1.00 AC: 3046 AN: 3046

Middle Eastern (MID) AF: 1.00 AC: 70 AN: 70

European-Non Finnish (NFE) AF: 0.991 AC: 12964 AN: 13077

Other (OTH) AF: 0.998 AC: 432 AN: 433

Alfa AF: 0.974 Hom.: 54400

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.30

Splicing

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

Other links and lift over

dbSNP: rs34173183; hg19: chrY-24405862;