rs16648

Positions:

• 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.12925843_12925844delAG		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;