rs9786712

chrY-12465377-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000381172.3(XGY1):n.184+3066C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0261 in 32,950 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., 859 hem., cov: 0)
• Consequence: XGY1 ENST00000381172.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

Genes affected

XGY1 (HGNC:12807): (XG Y-linked 1 (pseudogene))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XGY1	ENST00000381172.3	n.184+3066C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0260 AC: 856 AN: 32888 Hom.: 0 Cov.: 0 AF XY: 0.0260 AC XY: 856 AN XY: 32888

Gnomad AFR AF: 0.00500

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.0795

Gnomad EAS AF: 0.000812

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.000299

Gnomad MID AF: 0.205

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0256

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

GnomAD4 genome AF: 0.0261 AC: 859 AN: 32950 Hom.: 0 Cov.: 0 AF XY: 0.0261 AC XY: 859 AN XY: 32950

Gnomad4 AFR AF: 0.00497

Gnomad4 AMR AF: 0.0581

Gnomad4 ASJ AF: 0.0795

Gnomad4 EAS AF: 0.000812

Gnomad4 SAS AF: 0.0302

Gnomad4 FIN AF: 0.000299

Gnomad4 NFE AF: 0.0334

Gnomad4 OTH AF: 0.0254

Alfa AF: 0.0348 Hom.: 1319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	3.9

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9786712; hg19: chrY-14577177;