14-85216709-C-T

Variant names:

• chr14-85216709-C-T
• rs1550584
• ENST00000556016.1:n.210-13477G>A

Variant summary

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

The ENST00000556016.1(ENSG00000259044):​n.210-13477G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,952 control chromosomes in the GnomAD database, including 17,844 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 0.48 (17844 hom., cov: 33)
• Consequence: ENSG00000259044 ENST00000556016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

ENSG00000259044 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.537 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
ENSG00000259044	ENST00000556016.1	n.210-13477G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72283 AN: 151834 Hom.: 17839 Cov.: 33

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.476 AC: 72322 AN: 151952 Hom.: 17844 Cov.: 33 AF XY: 0.479 AC XY: 35570 AN XY: 74266

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.464

Alfa AF: 0.514 Hom.: 8611

Bravo AF: 0.452

Asia WGS AF: 0.361 AC: 1257 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1550584; hg19: chr14-85683053;