ENST00000550337.2:n.763-259T>C

Variant names:

• chr12-42616221-A-G
• rs4590936
• ENST00000550337.2:n.763-259T>C

Variant summary

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

The ENST00000550337.2(LINC02402):​n.763-259T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 152,124 control chromosomes in the GnomAD database, including 56,277 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 0.84 (56277 hom., cov: 31)
• Consequence: LINC02402 ENST00000550337.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 0 publications found

Genes affected

LINC02402 (HGNC:53329): (long intergenic non-protein coding RNA 2402)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000550337.2. 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
	LINC02402	NR_110042.1		n.753-259T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02402	ENST00000550337.2	TSL:1	n.763-259T>C		intron	N/A
	LINC02402	ENST00000662847.1		n.1493-259T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128382 AN: 152006 Hom.: 56259 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.954

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.844 AC: 128440 AN: 152124 Hom.: 56277 Cov.: 31 AF XY: 0.848 AC XY: 63049 AN XY: 74370

African (AFR) AF: 0.586 AC: 24316 AN: 41464

American (AMR) AF: 0.893 AC: 13658 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3139 AN: 3470

East Asian (EAS) AF: 0.900 AC: 4658 AN: 5176

South Asian (SAS) AF: 0.951 AC: 4580 AN: 4818

European-Finnish (FIN) AF: 0.975 AC: 10313 AN: 10574

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.953 AC: 64847 AN: 68010

Other (OTH) AF: 0.853 AC: 1805 AN: 2116

Alfa AF: 0.877 Hom.: 4186

Bravo AF: 0.825

Asia WGS AF: 0.905 AC: 3145 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.69
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs4590936; hg19: chr12-43010023;