Y-12974273-G-C

Position:

• chrY-12974273-G-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 0.026 (0 hom., 862 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0529 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

Frequencies

GnomAD3 genomes AF: 0.0261 AC: 860 AN: 32944 Hom.: 0 Cov.: 0 AF XY: 0.0261 AC XY: 860 AN XY: 32944

Gnomad AFR AF: 0.00519

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.000781

Gnomad SAS AF: 0.0310

Gnomad FIN AF: 0.000608

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.0328

Gnomad OTH AF: 0.0375

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

GnomAD4 genome AF: 0.0261 AC: 862 AN: 33007 Hom.: 0 Cov.: 0 AF XY: 0.0261 AC XY: 862 AN XY: 33007

Gnomad4 AFR AF: 0.00516

Gnomad4 AMR AF: 0.0594

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.000781

Gnomad4 SAS AF: 0.0316

Gnomad4 FIN AF: 0.000608

Gnomad4 NFE AF: 0.0329

Gnomad4 OTH AF: 0.0373

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.7

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7067251; hg19: chrY-15086183;