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. 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 0.026 (0 hom., 862 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0529 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

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

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

African (AFR) AF: 0.00516 AC: 44 AN: 8521

American (AMR) AF: 0.0594 AC: 214 AN: 3603

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 58 AN: 768

East Asian (EAS) AF: 0.000781 AC: 1 AN: 1280

South Asian (SAS) AF: 0.0316 AC: 46 AN: 1455

European-Finnish (FIN) AF: 0.000608 AC: 2 AN: 3287

Middle Eastern (MID) AF: 0.183 AC: 13 AN: 71

European-Non Finnish (NFE) AF: 0.0329 AC: 440 AN: 13361

Other (OTH) AF: 0.0373 AC: 17 AN: 456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.7
PhyloP100		0.17

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7067251;

hg19: chrY-15086183;