chr14-89787552-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000259053 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555070.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259053	ENST00000555070.1	TSL:3	n.170+166354G>A		intron	N/A

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

African (AFR) AF: 0.259 AC: 10751 AN: 41494

American (AMR) AF: 0.355 AC: 5421 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1453 AN: 3470

East Asian (EAS) AF: 0.0314 AC: 163 AN: 5184

South Asian (SAS) AF: 0.334 AC: 1610 AN: 4822

European-Finnish (FIN) AF: 0.433 AC: 4574 AN: 10572

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31069 AN: 67992

Other (OTH) AF: 0.382 AC: 807 AN: 2112

Alfa AF: 0.436 Hom.: 23808

Bravo AF: 0.361

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.059
DANN	Benign	0.18
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs8016216; hg19: chr14-90253896;