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).

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: 0.994 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 v4.3

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;