16-52548862-TAA-TA

Position:

• chr16-52548862-TAA-TA

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 0.36 (10854 hom., cov: 18)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.52548863delA		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54841 AN: 151572 Hom.: 10822 Cov.: 18

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.362 AC: 54934 AN: 151690 Hom.: 10854 Cov.: 18 AF XY: 0.365 AC XY: 27069 AN XY: 74116

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.361

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: rs45538731; hg19: chr16-52582774;