rs16648

Variant names:

• chrY-12925842-CAG-C
• rs16648

Your query was ambiguous. Multiple possible variants found:

• chrY-12925842-CAG-C
• chrY-12925842-CAG-CAGAG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.027 (0 hom., 908 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.053 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: 0.0265 AC: 905 AN: 34133 Hom.: 0 Cov.: 0 AF XY: 0.0265 AC XY: 905 AN XY: 34133

Gnomad AFR AF: 0.00560

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0822

Gnomad EAS AF: 0.000782

Gnomad SAS AF: 0.0337

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.192

Gnomad NFE AF: 0.0331

Gnomad OTH AF: 0.0327

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

GnomAD4 genome AF: 0.0266 AC: 908 AN: 34198 Hom.: 0 Cov.: 0 AF XY: 0.0266 AC XY: 908 AN XY: 34198

Gnomad4 AFR AF: 0.00556

Gnomad4 AMR AF: 0.0594

Gnomad4 ASJ AF: 0.0822

Gnomad4 EAS AF: 0.000782

Gnomad4 SAS AF: 0.0343

Gnomad4 FIN AF: 0.000283

Gnomad4 NFE AF: 0.0332

Gnomad4 OTH AF: 0.0325

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16648; hg19: chrY-15037754;