rs9786712

Variant names:

• chrY-12465377-G-A
• rs9786712

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: LOC124905301 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235
• Publications: 1 publications found

Genes affected

LOC124905301 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124905301		n.12465377G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XGY1	ENST00000381172.3	n.184+3066C>T		intron_variant	Intron 4 of 7	6

Frequencies

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

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

African (AFR) AF: 0.00497 AC: 42 AN: 8456

American (AMR) AF: 0.0581 AC: 208 AN: 3580

Ashkenazi Jewish (ASJ) AF: 0.0795 AC: 60 AN: 755

East Asian (EAS) AF: 0.000812 AC: 1 AN: 1231

South Asian (SAS) AF: 0.0302 AC: 43 AN: 1422

European-Finnish (FIN) AF: 0.000299 AC: 1 AN: 3346

Middle Eastern (MID) AF: 0.211 AC: 15 AN: 71

European-Non Finnish (NFE) AF: 0.0334 AC: 448 AN: 13414

Other (OTH) AF: 0.0254 AC: 12 AN: 472

Alfa AF: 0.0495 Hom.: 2429

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs9786712; hg19: chrY-14577177;