ENST00000513718.2:n.247-1497G>A

Variant names:

• chr4-159668155-C-T
• rs1117139
• ENST00000513718.2:n.247-1497G>A

Variant summary

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

The ENST00000513718.2(LINC02233):​n.247-1497G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.958 in 152,340 control chromosomes in the GnomAD database, including 69,957 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 0.96 (69957 hom., cov: 33)
• Consequence: LINC02233 ENST00000513718.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 1 publications found

Genes affected

LINC02233 (HGNC:53104): (long intergenic non-protein coding RNA 2233)

LOC107986324 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513718.2. 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
	LINC02233	NR_146278.1		n.203-1497G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02233	ENST00000513718.2	TSL:3	n.247-1497G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.958 AC: 145813 AN: 152222 Hom.: 69907 Cov.: 33

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.991

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.951

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

GnomAD4 genome AF: 0.958 AC: 145920 AN: 152340 Hom.: 69957 Cov.: 33 AF XY: 0.959 AC XY: 71434 AN XY: 74498

African (AFR) AF: 0.915 AC: 38036 AN: 41568

American (AMR) AF: 0.967 AC: 14805 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.978 AC: 3396 AN: 3472

East Asian (EAS) AF: 0.911 AC: 4716 AN: 5178

South Asian (SAS) AF: 0.961 AC: 4638 AN: 4826

European-Finnish (FIN) AF: 0.991 AC: 10529 AN: 10624

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.979 AC: 66602 AN: 68040

Other (OTH) AF: 0.951 AC: 2011 AN: 2114

Alfa AF: 0.970 Hom.: 8904

Bravo AF: 0.954

Asia WGS AF: 0.942 AC: 3278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.36
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1117139; hg19: chr4-160589307;