6-53312880-C-A

Variant names:

• chr6-53312880-C-A
• rs209489
• NM_021814.5:c.-8-17173G>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.-8-17173G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.92 in 152,274 control chromosomes in the GnomAD database, including 64,837 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 0.92 (64837 hom., cov: 32)
• Consequence: ELOVL5 NM_021814.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 11 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 = 0.972 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021814.5. 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
	ELOVL5	NM_021814.5	MANE Select	c.-8-17173G>T		intron	N/A	NP_068586.1
	ELOVL5	NM_001242828.2		c.-8-17173G>T		intron	N/A	NP_001229757.1
	ELOVL5	NM_001301856.2		c.-8-17173G>T		intron	N/A	NP_001288785.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL5	ENST00000304434.11	TSL:1 MANE Select	c.-8-17173G>T		intron	N/A	ENSP00000306640.6
	ELOVL5	ENST00000542638.5	TSL:1	c.-8-17173G>T		intron	N/A	ENSP00000440728.2
	ELOVL5	ENST00000370913.5	TSL:1	c.-8-17173G>T		intron	N/A	ENSP00000359951.5

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140060 AN: 152156 Hom.: 64785 Cov.: 32

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.920 AC: 140163 AN: 152274 Hom.: 64837 Cov.: 32 AF XY: 0.920 AC XY: 68498 AN XY: 74458

African (AFR) AF: 0.980 AC: 40762 AN: 41574

American (AMR) AF: 0.765 AC: 11688 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3169 AN: 3470

East Asian (EAS) AF: 0.955 AC: 4951 AN: 5182

South Asian (SAS) AF: 0.941 AC: 4541 AN: 4824

European-Finnish (FIN) AF: 0.951 AC: 10101 AN: 10616

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.913 AC: 62081 AN: 68020

Other (OTH) AF: 0.895 AC: 1892 AN: 2114

Alfa AF: 0.909 Hom.: 34991

Bravo AF: 0.904

Asia WGS AF: 0.943 AC: 3279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.90
DANN	Benign	0.67
PhyloP100		-0.33
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: rs209489; hg19: chr6-53177678;