16-52548862-TAA-TA

Variant names:

• chr16-52548862-TA-T
• rs45538731
• ENST00000826650.1:n.102+2351delA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000826650.1(ENSG00000285800):​n.102+2351delA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (10854 hom., cov: 18)
• Consequence: ENSG00000285800 ENST00000826650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724
• Publications: 1 publications found

Genes affected

ENSG00000285800 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285800	ENST00000826650.1	n.102+2351delA		intron_variant	Intron 1 of 2
ENSG00000285800	ENST00000826651.1	n.89+2351delA		intron_variant	Intron 1 of 5
ENSG00000285800	ENST00000826652.1	n.104+2303delA		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.499 AC: 20620 AN: 41322

American (AMR) AF: 0.382 AC: 5821 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1350 AN: 3468

East Asian (EAS) AF: 0.619 AC: 3194 AN: 5158

South Asian (SAS) AF: 0.266 AC: 1272 AN: 4788

European-Finnish (FIN) AF: 0.320 AC: 3359 AN: 10502

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.268 AC: 18166 AN: 67898

Other (OTH) AF: 0.361 AC: 760 AN: 2108

Alfa AF: 0.141 Hom.: 209

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs45538731; hg19: chr16-52582774;