6-53311967-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021814.5(ELOVL5):c.-8-16260C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,826 control chromosomes in the GnomAD database, including 27,323 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 (27323 hom., cov: 31)
• Consequence: ELOVL5 NM_021814.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• 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/exons	MANE	UniProt
ELOVL5	NM_021814.5	c.-8-16260C>A		intron_variant		ENST00000304434.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL5	ENST00000304434.11	c.-8-16260C>A		intron_variant		1	NM_021814.5	P1

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86479 AN: 151706 Hom.: 27265 Cov.: 31

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.570 AC: 86601 AN: 151826 Hom.: 27323 Cov.: 31 AF XY: 0.562 AC XY: 41666 AN XY: 74180

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.568

Alfa AF: 0.483 Hom.: 8539

Bravo AF: 0.602

Asia WGS AF: 0.463 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.5
Dann	Benign	0.18

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: rs9395855; hg19: chr6-53176765;