rs2980300

Variant names:

• chr1-850609-T-A
• rs2980300
• ENST00000445118.7:n.281-1318T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-850609-T-A
• chr1-850609-T-C
• chr1-850609-T-G

Variant summary

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

The ENST00000610067.8(LINC01128):​n.1550T>A variant causes a non coding transcript exon 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: LINC01128 ENST00000610067.8 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880
• Publications: 6 publications found

Genes affected

LINC01128 (HGNC:49377): (long intergenic non-protein coding RNA 1128)

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=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000610067.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01128	NR_047519.1		n.441-1318T>A		intron	N/A
	LINC01128	NR_047521.1		n.288-1318T>A		intron	N/A
	LINC01128	NR_047523.1		n.288-1318T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01128	ENST00000445118.7	TSL:1	n.281-1318T>A		intron	N/A
	LINC01128	ENST00000449005.8	TSL:1	n.422-1318T>A		intron	N/A
	LINC01128	ENST00000610067.8	TSL:4	n.1550T>A		non_coding_transcript_exon	Exon 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

Alfa AF: 0.00 Hom.: 18429

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.51
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2980300; hg19: chr1-785989;