rs9393681

Variant names:

• chr6-26008032-T-A
• rs9393681
• ENST00000730115.1:n.561+9747T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-26008032-T-A
• chr6-26008032-T-C

Variant summary

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

The ENST00000730115.1(LINC02980):​n.561+9747T>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: 32)
• Consequence: LINC02980 ENST00000730115.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 17 publications found

Genes affected

LINC02980 (HGNC:56046): (long intergenic non-protein coding RNA 2980)

ENSG00000272558 (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=-0.77).

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
LINC02980	ENST00000730115.1	n.561+9747T>A		intron_variant	Intron 2 of 2
LINC02980	ENST00000730116.1	n.486+9747T>A		intron_variant	Intron 3 of 3
LINC02980	ENST00000730117.1	n.576-6514T>A		intron_variant	Intron 3 of 3
ENSG00000272558	ENST00000730234.1	n.84+6048A>T		intron_variant	Intron 2 of 3

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

Alfa AF: 0.00 Hom.: 20223

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.9
DANN	Benign	0.59
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs9393681; hg19: chr6-26008260;