rs1125978

chrY-13163289-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2 BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0257 in 32,574 control chromosomes in the GnomAD database, with no homozygous occurrence. 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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• 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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Hemizygotes in GnomAd at 835 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0257 AC: 835 AN: 32509 Hom.: 0 Cov.: 0 AF XY: 0.0257 AC XY: 835 AN XY: 32509

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

Gnomad4 AFR AF: 0.00527

Gnomad4 AMR AF: 0.0556

Gnomad4 ASJ AF: 0.0763

Gnomad4 EAS AF: 0.000801

Gnomad4 SAS AF: 0.0341

Gnomad4 FIN AF: 0.000305

Gnomad4 NFE AF: 0.0329

Gnomad4 OTH AF: 0.0270

Alfa AF: 0.964 Hom.: 570

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1125978; hg19: chrY-15275200;