rs9786640

Variant names:

• chrY-12527496-A-C
• rs9786640

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 0.027 (0 hom., 877 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

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

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

African (AFR) AF: 0.00564 AC: 47 AN: 8338

American (AMR) AF: 0.0591 AC: 204 AN: 3453

Ashkenazi Jewish (ASJ) AF: 0.0768 AC: 58 AN: 755

East Asian (EAS) AF: 0.000804 AC: 1 AN: 1244

South Asian (SAS) AF: 0.0342 AC: 48 AN: 1405

European-Finnish (FIN) AF: 0.000312 AC: 1 AN: 3204

Middle Eastern (MID) AF: 0.203 AC: 14 AN: 69

European-Non Finnish (NFE) AF: 0.0345 AC: 457 AN: 13250

Other (OTH) AF: 0.0357 AC: 16 AN: 448

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
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs9786640; hg19: chrY-14639427;