rs2016740

Variant names:

• chr4-111959258-C-A
• rs2016740
• ENST00000508010.2:n.194+61156G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-111959258-C-A
• chr4-111959258-C-G
• chr4-111959258-C-T

Variant summary

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

The ENST00000511219.1(LINC02945):​n.134+113307G>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: 32)
• Consequence: LINC02945 ENST00000511219.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 6 publications found

Genes affected

LINC02945 (HGNC:55960): (long intergenic non-protein coding RNA 2945)

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=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511219.1. 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
	LINC02945	NR_186680.1		n.98+113307G>T		intron	N/A
	LINC02945	NR_186681.1		n.184+61156G>T		intron	N/A
	LINC02945	NR_186682.1		n.83-130208G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02945	ENST00000508010.2	TSL:5	n.194+61156G>T		intron	N/A
	LINC02945	ENST00000511219.1	TSL:3	n.134+113307G>T		intron	N/A
	LINC02945	ENST00000679735.2		n.187+61156G>T		intron	N/A

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.5
DANN	Benign	0.71
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2016740; hg19: chr4-112880414;