5-60833534-A-C

Variant names:

• chr5-60833534-A-C
• rs6869332
• NM_024930.3:c.-86+10626T>G

Variant summary

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

The NM_024930.3(ELOVL7):​c.-86+10626T>G 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: 30)
• Consequence: ELOVL7 NM_024930.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 7 publications found

Genes affected

ELOVL7 (HGNC:26292): (ELOVL fatty acid elongase 7) Enables fatty acid elongase activity. Involved in fatty acid elongation, polyunsaturated fatty acid; fatty acid elongation, saturated fatty acid; and very long-chain fatty acid biosynthetic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024930.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL7	NM_024930.3	MANE Select	c.-86+10626T>G		intron	N/A	NP_079206.2
	ELOVL7	NM_001104558.2		c.-35+10626T>G		intron	N/A	NP_001098028.1
	ELOVL7	NM_001297617.2		c.-472+10626T>G		intron	N/A	NP_001284546.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL7	ENST00000508821.6	TSL:1 MANE Select	c.-86+10626T>G		intron	N/A	ENSP00000424123.1
	ELOVL7	ENST00000505959.5	TSL:1	c.-472+10626T>G		intron	N/A	ENSP00000421043.1
	ELOVL7	ENST00000425382.5	TSL:5	c.-35+10626T>G		intron	N/A	ENSP00000402634.1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		0.18

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6869332; hg19: chr5-60129361;