ENST00000522554.2:n.600+12202G>A

Variant names:

• chr4-184612537-C-T
• rs7675251
• ENST00000522554.2:n.600+12202G>A

Variant summary

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

The ENST00000522554.2(LINC02365):​n.600+12202G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,156 control chromosomes in the GnomAD database, including 53,049 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 0.82 (53049 hom., cov: 32)
• Consequence: LINC02365 ENST00000522554.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 3 publications found

Genes affected

LINC02365 (HGNC:53285): (long intergenic non-protein coding RNA 2365)

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 = 0.933 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522554.2. 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
	LINC02365	NR_131967.1		n.134+12202G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02365	ENST00000522554.2	TSL:2	n.600+12202G>A		intron	N/A
	LINC02365	ENST00000765666.1		n.477+12202G>A		intron	N/A
	LINC02365	ENST00000765667.1		n.602+12202G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124899 AN: 152038 Hom.: 53031 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.961

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.914

Gnomad NFE AF: 0.939

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.821 AC: 124953 AN: 152156 Hom.: 53049 Cov.: 32 AF XY: 0.811 AC XY: 60320 AN XY: 74400

African (AFR) AF: 0.715 AC: 29651 AN: 41472

American (AMR) AF: 0.724 AC: 11068 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3268 AN: 3472

East Asian (EAS) AF: 0.284 AC: 1467 AN: 5174

South Asian (SAS) AF: 0.716 AC: 3456 AN: 4824

European-Finnish (FIN) AF: 0.873 AC: 9247 AN: 10596

Middle Eastern (MID) AF: 0.918 AC: 268 AN: 292

European-Non Finnish (NFE) AF: 0.939 AC: 63854 AN: 68022

Other (OTH) AF: 0.851 AC: 1798 AN: 2112

Alfa AF: 0.897 Hom.: 163816

Bravo AF: 0.804

Asia WGS AF: 0.545 AC: 1899 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	0.37
DANN	Benign	0.26
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7675251; hg19: chr4-185533691;