rs13325788

Variant names:

• chr3-138943768-G-A
• rs13325788
• ENST00000477059.2:n.49+198C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-138943768-G-A
• chr3-138943768-G-T

Variant summary

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

The ENST00000477059.2(LINC01391):​n.49+198C>T 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: LINC01391 ENST00000477059.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467
• Publications: 1 publications found

Genes affected

LINC01391 (HGNC:50666): (long intergenic non-protein coding RNA 1391)

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=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01391	NR_121649.1	n.55+198C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01391	ENST00000477059.2	n.49+198C>T		intron_variant	Intron 1 of 2	3
LINC01391	ENST00000483650.1	n.38+198C>T		intron_variant	Intron 1 of 2	3
LINC01391	ENST00000495287.1	n.55+198C>T		intron_variant	Intron 1 of 2	2
LINC01391	ENST00000774123.1	n.46+198C>T		intron_variant	Intron 1 of 2

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.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.6
DANN	Benign	0.69
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs13325788; hg19: chr3-138662610;