14-55269155-T-G

Variant names:

• chr14-55269155-T-G
• rs6573013
• ENST00000554650.1:n.164+1990A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000556183.2(FBXO34-AS1):​n.197+2727A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,982 control chromosomes in the GnomAD database, including 26,749 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 0.56 (26749 hom., cov: 31)
• Consequence: FBXO34-AS1 ENST00000556183.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794
• Publications: 8 publications found

Genes affected

FBXO34-AS1 (HGNC:55450): (FBXO34 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556183.2. 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
	FBXO34-AS1	NR_184222.1		n.197+2727A>C		intron	N/A
	FBXO34-AS1	NR_184223.1		n.158+1990A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBXO34-AS1	ENST00000554650.1	TSL:3	n.164+1990A>C		intron	N/A
	FBXO34-AS1	ENST00000556183.2	TSL:2	n.197+2727A>C		intron	N/A
	FBXO34-AS1	ENST00000660805.1		n.166+1990A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84873 AN: 151864 Hom.: 26689 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.559 AC: 84994 AN: 151982 Hom.: 26749 Cov.: 31 AF XY: 0.558 AC XY: 41400 AN XY: 74254

African (AFR) AF: 0.872 AC: 36172 AN: 41482

American (AMR) AF: 0.410 AC: 6265 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1306 AN: 3472

East Asian (EAS) AF: 0.392 AC: 2025 AN: 5164

South Asian (SAS) AF: 0.478 AC: 2305 AN: 4818

European-Finnish (FIN) AF: 0.547 AC: 5755 AN: 10526

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29609 AN: 67926

Other (OTH) AF: 0.491 AC: 1038 AN: 2112

Alfa AF: 0.512 Hom.: 3872

Bravo AF: 0.558

Asia WGS AF: 0.497 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.40
DANN	Benign	0.80
PhyloP100		-0.79

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: rs6573013;

hg19: chr14-55735873;