14-85216709-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000259044 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556016.1. 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
	ENSG00000259044	ENST00000556016.1	TSL:3	n.210-13477G>A		intron	N/A

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

African (AFR) AF: 0.396 AC: 16407 AN: 41434

American (AMR) AF: 0.393 AC: 5995 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1617 AN: 3472

East Asian (EAS) AF: 0.261 AC: 1350 AN: 5178

South Asian (SAS) AF: 0.467 AC: 2254 AN: 4822

European-Finnish (FIN) AF: 0.597 AC: 6281 AN: 10528

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36797 AN: 67954

Other (OTH) AF: 0.464 AC: 981 AN: 2112

Alfa AF: 0.503 Hom.: 41669

Bravo AF: 0.452

Asia WGS AF: 0.361 AC: 1257 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.33
PhyloP100		-1.7

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: rs1550584;

hg19: chr14-85683053;