rs28463809

Variant names:

• chr16-52549142-G-T
• rs28463809
• ENST00000826650.1:n.102+2630G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000826650.1(ENSG00000285800):​n.102+2630G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,062 control chromosomes in the GnomAD database, including 11,274 homozygotes. 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 0.37 (11274 hom., cov: 32)
• Consequence: ENSG00000285800 ENST00000826650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 5 publications found

Genes affected

ENSG00000285800 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 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+2630G>T		intron_variant	Intron 1 of 2
ENSG00000285800	ENST00000826651.1	n.89+2630G>T		intron_variant	Intron 1 of 5
ENSG00000285800	ENST00000826652.1	n.104+2582G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55709 AN: 151942 Hom.: 11241 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.367 AC: 55808 AN: 152062 Hom.: 11274 Cov.: 32 AF XY: 0.369 AC XY: 27460 AN XY: 74320

African (AFR) AF: 0.518 AC: 21482 AN: 41470

American (AMR) AF: 0.384 AC: 5864 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1350 AN: 3472

East Asian (EAS) AF: 0.621 AC: 3199 AN: 5154

South Asian (SAS) AF: 0.250 AC: 1206 AN: 4830

European-Finnish (FIN) AF: 0.318 AC: 3364 AN: 10578

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18188 AN: 67986

Other (OTH) AF: 0.362 AC: 760 AN: 2100

Alfa AF: 0.300 Hom.: 5357

Bravo AF: 0.383

Asia WGS AF: 0.428 AC: 1487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.67
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs28463809; hg19: chr16-52583054;