rs16878913

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000288035 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000288035	ENST00000666280.1	n.649+5613T>A		intron_variant	Intron 3 of 3

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

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.365

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16878913; hg19: chr5-50774090;