rs7067251

Variant names:

• chrY-12974273-G-C
• rs7067251

Your query was ambiguous. Multiple possible variants found:

• chrY-12974273-G-C
• chrY-12974273-G-T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;