chr16-52549498-G-A

Variant names:

• chr16-52549498-G-A
• rs45465998
• ENST00000826650.1:n.102+2986G>A

Variant summary

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

The ENST00000826650.1(ENSG00000285800):​n.102+2986G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 146,070 control chromosomes in the GnomAD database, including 7,196 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 0.31 (7196 hom., cov: 27)
• Consequence: ENSG00000285800 ENST00000826650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826650.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285800	ENST00000826650.1		n.102+2986G>A		intron	N/A
	ENSG00000285800	ENST00000826651.1		n.89+2986G>A		intron	N/A
	ENSG00000285800	ENST00000826652.1		n.104+2938G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.306 AC: 44680 AN: 145998 Hom.: 7182 Cov.: 27

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.306 AC: 44730 AN: 146070 Hom.: 7196 Cov.: 27 AF XY: 0.306 AC XY: 21658 AN XY: 70716

African (AFR) AF: 0.392 AC: 15421 AN: 39312

American (AMR) AF: 0.347 AC: 5037 AN: 14524

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1092 AN: 3436

East Asian (EAS) AF: 0.473 AC: 2282 AN: 4820

South Asian (SAS) AF: 0.210 AC: 964 AN: 4590

European-Finnish (FIN) AF: 0.252 AC: 2320 AN: 9222

Middle Eastern (MID) AF: 0.343 AC: 94 AN: 274

European-Non Finnish (NFE) AF: 0.248 AC: 16619 AN: 66948

Other (OTH) AF: 0.314 AC: 645 AN: 2054

Alfa AF: 0.272 Hom.: 8373

Bravo AF: 0.323

Asia WGS AF: 0.334 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.031
DANN	Benign	0.71
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs45465998; hg19: chr16-52583410;