rs7170668

Variant names:

• chr15-95470914-T-A
• rs7170668
• ENST00000554837.5:n.337+17041T>A

Your query was ambiguous. Multiple possible variants found:

• chr15-95470914-T-A
• chr15-95470914-T-C

Variant summary

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

The ENST00000554837.5(LINC00924):​n.337+17041T>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: LINC00924 ENST00000554837.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834
• Publications: 7 publications found

Genes affected

LINC00924 (HGNC:27081): (long intergenic non-protein coding RNA 924)

ENSG00000258489 (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=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554837.5. 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
	LINC00924	NR_027132.1		n.339+17041T>A		intron	N/A
	LINC00924	NR_027133.1		n.339+17041T>A		intron	N/A
	LOC105370993	NR_188325.1		n.186-6105A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00924	ENST00000554837.5	TSL:1	n.337+17041T>A		intron	N/A
	ENSG00000258489	ENST00000554412.3	TSL:2	n.131-6105A>T		intron	N/A
	LINC00924	ENST00000556053.2	TSL:2	n.337+17041T>A		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

Alfa AF: 0.00 Hom.: 20624

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.9
DANN	Benign	0.68
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs7170668; hg19: chr15-96014143;