rs9786460

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000291034 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291034	ENST00000651802.1	n.451-61723C>T		intron_variant	Intron 4 of 9
ENSG00000291034	ENST00000651835.1	n.320-45100C>T		intron_variant	Intron 3 of 6

Frequencies

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

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

Gnomad4 AFR AF: 0.00509

Gnomad4 AMR AF: 0.0576

Gnomad4 ASJ AF: 0.0798

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0312

Gnomad4 FIN AF: 0.000297

Gnomad4 NFE AF: 0.0338

Gnomad4 OTH AF: 0.0373

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9786460; hg19: chrY-14423856;