rs2115564

Variant names:

• chr6-53308684-C-A
• rs2115564
• NM_021814.5:c.-8-12977G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021814.5(ELOVL5):​c.-8-12977G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,778 control chromosomes in the GnomAD database, including 27,218 homozygotes. 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: 𝑓 0.57 (27218 hom., cov: 29)
• Consequence: ELOVL5 NM_021814.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 2 publications found

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]

ELOVL5 Gene-Disease associations (from GenCC):

• spinocerebellar ataxia type 38

  Inheritance: AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL5	NM_021814.5	c.-8-12977G>T		intron_variant	Intron 1 of 7	ENST00000304434.11	NP_068586.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL5	ENST00000304434.11	c.-8-12977G>T		intron_variant	Intron 1 of 7	1	NM_021814.5	ENSP00000306640.6

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86155 AN: 151660 Hom.: 27160 Cov.: 29

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.568 AC: 86279 AN: 151778 Hom.: 27218 Cov.: 29 AF XY: 0.560 AC XY: 41514 AN XY: 74158

African (AFR) AF: 0.866 AC: 35853 AN: 41380

American (AMR) AF: 0.540 AC: 8233 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1809 AN: 3464

East Asian (EAS) AF: 0.401 AC: 2073 AN: 5166

South Asian (SAS) AF: 0.438 AC: 2098 AN: 4792

European-Finnish (FIN) AF: 0.345 AC: 3624 AN: 10498

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.453 AC: 30763 AN: 67908

Other (OTH) AF: 0.568 AC: 1200 AN: 2114

Alfa AF: 0.517 Hom.: 2738

Bravo AF: 0.600

Asia WGS AF: 0.459 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2115564; hg19: chr6-53173482;