rs9786460

Variant names:

• chrY-12303131-G-A
• rs9786460
• ENST00000651802.1:n.451-61723C>T

Variant summary

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

The ENST00000651802.1(ENSG00000291034):​n.451-61723C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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., 871 hem., cov: 0)
• Consequence: ENSG00000291034 ENST00000651802.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 1 publications found

Genes affected

ENSG00000291034 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651802.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000291034	ENST00000651802.1		n.451-61723C>T		intron	N/A
	ENSG00000291034	ENST00000651835.1		n.320-45100C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0264 AC: 868 AN: 32902 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00512

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0577

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.000297

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.0337

Gnomad OTH AF: 0.0375

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

GnomAD4 genome AF: 0.0264 AC: 871 AN: 32967 Hom.: 0 Cov.: 0 AF XY: 0.0264 AC XY: 871 AN XY: 32967

African (AFR) AF: 0.00509 AC: 43 AN: 8448

American (AMR) AF: 0.0576 AC: 205 AN: 3559

Ashkenazi Jewish (ASJ) AF: 0.0798 AC: 61 AN: 764

East Asian (EAS) AF: 0.00 AC: 0 AN: 1237

South Asian (SAS) AF: 0.0312 AC: 44 AN: 1410

European-Finnish (FIN) AF: 0.000297 AC: 1 AN: 3364

Middle Eastern (MID) AF: 0.206 AC: 14 AN: 68

European-Non Finnish (NFE) AF: 0.0338 AC: 455 AN: 13452

Other (OTH) AF: 0.0373 AC: 17 AN: 456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs9786460; hg19: chrY-14423856;