rs2202445

Variant names:

• chr5-7328063-G-A
• rs2202445
• ENST00000715908.1:n.369+13148G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-7328063-G-A
• chr5-7328063-G-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000715908.1(LINC02142):​n.369+13148G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: LINC02142 ENST00000715908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540
• Publications: 1 publications found

Genes affected

LINC02142 (HGNC:53002): (long intergenic non-protein coding RNA 2142)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02142	ENST00000715908.1	n.369+13148G>A		intron_variant	Intron 3 of 4
LINC02142	ENST00000715909.1	n.147+13148G>A		intron_variant	Intron 2 of 3
LINC02142	ENST00000838839.1	n.175+13148G>A		intron_variant	Intron 2 of 2
LINC02142	ENST00000838840.1	n.349+13148G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 137

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.73
PhyloP100		0.054

Splicing

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

Other links and lift over

dbSNP: rs2202445; hg19: chr5-7328176;