rs8016216

Variant names:

• chr14-89787552-C-T
• rs8016216
• ENST00000555070.1:n.170+166354G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000555070.1(ENSG00000259053):​n.170+166354G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,138 control chromosomes in the GnomAD database, including 11,437 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 (11437 hom., cov: 33)
• Consequence: ENSG00000259053 ENST00000555070.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

ENSG00000259053 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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
ENSG00000259053	ENST00000555070.1	n.170+166354G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56405 AN: 152020 Hom.: 11442 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.0310

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.371 AC: 56408 AN: 152138 Hom.: 11437 Cov.: 33 AF XY: 0.367 AC XY: 27268 AN XY: 74384

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.0314

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.382

Alfa AF: 0.437 Hom.: 20202

Bravo AF: 0.361

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.059
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8016216; hg19: chr14-90253896;