NM_021814.5:c.757-184_757-181delAAAA

Variant names:

• chr6-53269450-CTTTT-C
• rs3215545
• NM_021814.5:c.757-184_757-181delAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_021814.5(ELOVL5):​c.757-184_757-181delAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000679 in 147,344 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0000068 (0 hom., cov: 32)
• Consequence: ELOVL5 NM_021814.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381

Genes affected

ELOVL5 (HGNC:21308): (ELOVL fatty acid elongase 5) This gene belongs to the ELO family. It is highly expressed in the adrenal gland and testis, and encodes a multi-pass membrane protein that is localized in the endoplasmic reticulum. This protein is involved in the elongation of long-chain polyunsaturated fatty acids. Mutations in this gene have been associated with spinocerebellar ataxia-38 (SCA38). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL5	NM_021814.5	c.757-184_757-181delAAAA		intron_variant	Intron 7 of 7	ENST00000304434.11	NP_068586.1
ELOVL5	NM_001242828.2	c.838-184_838-181delAAAA		intron_variant	Intron 8 of 8		NP_001229757.1
ELOVL5	NM_001301856.2	c.757-184_757-181delAAAA		intron_variant	Intron 7 of 7		NP_001288785.1
ELOVL5	NM_001242830.2	c.632-184_632-181delAAAA		intron_variant	Intron 6 of 6		NP_001229759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL5	ENST00000304434.11	c.757-184_757-181delAAAA		intron_variant	Intron 7 of 7	1	NM_021814.5	ENSP00000306640.6
ELOVL5	ENST00000542638.5	c.632-184_632-181delAAAA		intron_variant	Intron 6 of 6	1		ENSP00000440728.2
ELOVL5	ENST00000370918.8	c.838-184_838-181delAAAA		intron_variant	Intron 8 of 8	2		ENSP00000359956.5

Frequencies

GnomAD3 genomes AF: 0.00000679 AC: 1 AN: 147344 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000151

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000679 AC: 1 AN: 147344 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 71744

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000151

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3215545; hg19: chr6-53134248;