rs9786640

Positions:

• chrY-12527496-A-C

Variant summary

Our verdict is Benign. Variant got -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 0.027 (0 hom., 877 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0270 AC: 874 AN: 32326 Hom.: 0 Cov.: 0 AF XY: 0.0270 AC XY: 874 AN XY: 32326

Gnomad AFR AF: 0.00567

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0592

Gnomad ASJ AF: 0.0768

Gnomad EAS AF: 0.000803

Gnomad SAS AF: 0.0335

Gnomad FIN AF: 0.000312

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.0343

Gnomad OTH AF: 0.0357

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

GnomAD4 genome AF: 0.0271 AC: 877 AN: 32378 Hom.: 0 Cov.: 0 AF XY: 0.0271 AC XY: 877 AN XY: 32378

Gnomad4 AFR AF: 0.00564

Gnomad4 AMR AF: 0.0591

Gnomad4 ASJ AF: 0.0768

Gnomad4 EAS AF: 0.000804

Gnomad4 SAS AF: 0.0342

Gnomad4 FIN AF: 0.000312

Gnomad4 NFE AF: 0.0345

Gnomad4 OTH AF: 0.0357

Alfa AF: 0.00549 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.079

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9786640; hg19: chrY-14639427;