rs9786460

Positions:

• chrY-12303131-G-A

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, non coding transcript 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: ENST00000651802.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651802.1	n.451-61723C>T		intron_variant, non_coding_transcript_variant
	ENST00000651835.1	n.320-45100C>T		intron_variant, non_coding_transcript_variant

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;