rs34134567

Variant names:

• chrY-13493019-C-T
• rs34134567

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

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 0.019 (0 hom., 638 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0194 (638/32841) while in subpopulation AMR AF = 0.0442 (158/3578). AF 95% confidence interval is 0.0385. There are 0 homozygotes in GnomAd4. There are 638 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Hemizygotes in GnomAd4 at 638 gene

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: 0.0194 AC: 635 AN: 32780 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00405

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0442

Gnomad ASJ AF: 0.00797

Gnomad EAS AF: 0.000792

Gnomad SAS AF: 0.0129

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.176

Gnomad NFE AF: 0.0281

Gnomad OTH AF: 0.0133

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

GnomAD4 genome AF: 0.0194 AC: 638 AN: 32841 Hom.: 0 Cov.: 0 AF XY: 0.0194 AC XY: 638 AN XY: 32841

African (AFR) AF: 0.00403 AC: 34 AN: 8437

American (AMR) AF: 0.0442 AC: 158 AN: 3578

Ashkenazi Jewish (ASJ) AF: 0.00797 AC: 6 AN: 753

East Asian (EAS) AF: 0.000792 AC: 1 AN: 1262

South Asian (SAS) AF: 0.0135 AC: 20 AN: 1482

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3212

Middle Eastern (MID) AF: 0.178 AC: 13 AN: 73

European-Non Finnish (NFE) AF: 0.0282 AC: 378 AN: 13385

Other (OTH) AF: 0.0132 AC: 6 AN: 454

Alfa AF: 0.0440 Hom.: 2580

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.56
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs34134567; hg19: chrY-15604899; COSMIC: COSV57691162;