rs1943816

Variant names:

• chr18-73391387-A-C
• rs1943816
• ENST00000786158.1:n.630-430A>C

Your query was ambiguous. Multiple possible variants found:

• chr18-73391387-A-C
• chr18-73391387-A-G
• chr18-73391387-A-T

Variant summary

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

The ENST00000786158.1(LINC02582):​n.630-430A>C 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: 32)
• Consequence: LINC02582 ENST00000786158.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 0 publications found

Genes affected

LINC02582 (HGNC:53792): (long intergenic non-protein coding RNA 2582)

LOC105372190 (HGNC:):

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=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372190	XR_007066468.1	n.1384+9025T>G		intron_variant	Intron 6 of 6
LOC105372190	XR_007066469.1	n.1491+9025T>G		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02582	ENST00000786158.1	n.630-430A>C		intron_variant	Intron 5 of 5
LINC02582	ENST00000786159.1	n.718-430A>C		intron_variant	Intron 4 of 4
LINC02582	ENST00000786160.1	n.716-430A>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.69
DANN	Benign	0.73
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1943816; hg19: chr18-71058622;