rs1125978

Variant names:

• chrY-13163289-C-G
• rs1125978

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 0.026 (0 hom., 838 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0257 (838/32574) while in subpopulation AMR AF = 0.0556 (193/3471). AF 95% confidence interval is 0.0492. There are 0 homozygotes in GnomAd4. There are 838 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Hemizygotes in GnomAd4 at 838 gene

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: 0.0257 AC: 835 AN: 32509 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00531

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0557

Gnomad ASJ AF: 0.0763

Gnomad EAS AF: 0.000800

Gnomad SAS AF: 0.0335

Gnomad FIN AF: 0.000305

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.0327

Gnomad OTH AF: 0.0273

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

GnomAD4 genome AF: 0.0257 AC: 838 AN: 32574 Hom.: 0 Cov.: 0 AF XY: 0.0257 AC XY: 838 AN XY: 32574

African (AFR) AF: 0.00527 AC: 44 AN: 8344

American (AMR) AF: 0.0556 AC: 193 AN: 3471

Ashkenazi Jewish (ASJ) AF: 0.0763 AC: 58 AN: 760

East Asian (EAS) AF: 0.000801 AC: 1 AN: 1249

South Asian (SAS) AF: 0.0341 AC: 48 AN: 1408

European-Finnish (FIN) AF: 0.000305 AC: 1 AN: 3281

Middle Eastern (MID) AF: 0.205 AC: 15 AN: 73

European-Non Finnish (NFE) AF: 0.0329 AC: 438 AN: 13332

Other (OTH) AF: 0.0270 AC: 12 AN: 444

Alfa AF: 0.964 Hom.: 570

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.3
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs1125978; hg19: chrY-15275200;