rs16878913

Variant names:

• chr5-51478256-A-T
• rs16878913
• ENST00000666280.1:n.649+5613T>A

Variant summary

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

The ENST00000666280.1(ENSG00000288035):​n.649+5613T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,888 control chromosomes in the GnomAD database, including 13,364 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 0.40 (13364 hom., cov: 31)
• Consequence: ENSG00000288035 ENST00000666280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 1 publications found

Genes affected

ENSG00000288035 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666280.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288035	ENST00000666280.1		n.649+5613T>A		intron	N/A
	ENSG00000288035	ENST00000730931.1		n.324+5613T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61260 AN: 151766 Hom.: 13342 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.404 AC: 61339 AN: 151888 Hom.: 13364 Cov.: 31 AF XY: 0.399 AC XY: 29627 AN XY: 74228

African (AFR) AF: 0.576 AC: 23842 AN: 41424

American (AMR) AF: 0.366 AC: 5580 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1091 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1098 AN: 5138

South Asian (SAS) AF: 0.271 AC: 1308 AN: 4822

European-Finnish (FIN) AF: 0.366 AC: 3859 AN: 10556

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.345 AC: 23429 AN: 67914

Other (OTH) AF: 0.365 AC: 771 AN: 2114

Alfa AF: 0.385 Hom.: 1464

Bravo AF: 0.412

Asia WGS AF: 0.285 AC: 990 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.85
DANN	Benign	0.78
PhyloP100		-0.63

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16878913;

hg19: chr5-50774090;