rs1138244

Variant names:

• chr6-106769806-T-C
• rs1138244
• ENST00000415714.5:n.73+17677A>G

Variant summary

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

The ENST00000415714.5(LINC02532):​n.73+17677A>G 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: 31)
• Consequence: LINC02532 ENST00000415714.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.918
• Publications: 1 publications found

Genes affected

LINC02532 (HGNC:53549): (long intergenic non-protein coding RNA 2532)

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=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02532	NR_033557.2	n.283+17453A>G		intron_variant	Intron 1 of 6
LINC02532	NR_147986.1	n.284-13545A>G		intron_variant	Intron 1 of 3
LINC02532	NR_147987.1	n.283+17453A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02532	ENST00000415714.5	n.73+17677A>G		intron_variant	Intron 1 of 2	3
LINC02532	ENST00000427903.6	n.124-13349A>G		intron_variant	Intron 1 of 5	3
LINC02532	ENST00000428750.6	n.183+17477A>G		intron_variant	Intron 1 of 6	5

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.1
DANN	Benign	0.49
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs1138244; hg19: chr6-107217681;