6-53289156-C-A

Variant names:

• chr6-53289156-C-A
• rs2294867
• NM_021814.5:c.246+2620G>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.246+2620G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,098 control chromosomes in the GnomAD database, including 15,772 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 0.44 (15772 hom., cov: 33)
• Consequence: ELOVL5 NM_021814.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 8 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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL5	NM_021814.5	c.246+2620G>T		intron_variant	Intron 3 of 7	ENST00000304434.11	NP_068586.1
ELOVL5	NM_001242828.2	c.247-1214G>T		intron_variant	Intron 3 of 8		NP_001229757.1
ELOVL5	NM_001301856.2	c.246+2620G>T		intron_variant	Intron 3 of 7		NP_001288785.1
ELOVL5	NM_001242830.2	c.246+2620G>T		intron_variant	Intron 3 of 6		NP_001229759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL5	ENST00000304434.11	c.246+2620G>T		intron_variant	Intron 3 of 7	1	NM_021814.5	ENSP00000306640.6

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66729 AN: 151980 Hom.: 15742 Cov.: 33

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.439 AC: 66813 AN: 152098 Hom.: 15772 Cov.: 33 AF XY: 0.432 AC XY: 32085 AN XY: 74342

African (AFR) AF: 0.615 AC: 25505 AN: 41490

American (AMR) AF: 0.459 AC: 7015 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1655 AN: 3464

East Asian (EAS) AF: 0.416 AC: 2150 AN: 5172

South Asian (SAS) AF: 0.421 AC: 2032 AN: 4824

European-Finnish (FIN) AF: 0.240 AC: 2535 AN: 10568

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24384 AN: 67982

Other (OTH) AF: 0.463 AC: 977 AN: 2112

Alfa AF: 0.417 Hom.: 2977

Bravo AF: 0.466

Asia WGS AF: 0.432 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.3
DANN	Benign	0.46
PhyloP100		0.14
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: rs2294867; hg19: chr6-53153954;