6-53302038-T-C

Position:

• chr6-53302038-T-C

Variant summary

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

The NM_021814.5(ELOVL5):​c.-8-6331A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,036 control chromosomes in the GnomAD database, including 11,108 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 0.36 (11108 hom., cov: 32)
• Consequence: ELOVL5 NM_021814.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.45

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELOVL5	NM_021814.5	c.-8-6331A>G		intron_variant		ENST00000304434.11	NP_068586.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELOVL5	ENST00000304434.11	c.-8-6331A>G		intron_variant		1	NM_021814.5	ENSP00000306640	P1

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55116 AN: 151918 Hom.: 11102 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.363 AC: 55160 AN: 152036 Hom.: 11108 Cov.: 32 AF XY: 0.355 AC XY: 26425 AN XY: 74346

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.363

Alfa AF: 0.310 Hom.: 7298

Bravo AF: 0.370

Asia WGS AF: 0.378 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.0040
DANN	Benign	0.53

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: rs761179; hg19: chr6-53166836;