6-53278756-T-C

Position:

• chr6-53278756-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.247-2500A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,994 control chromosomes in the GnomAD database, including 7,423 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 0.29 (7423 hom., cov: 32)
• Consequence: ELOVL5 NM_021814.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELOVL5	NM_021814.5	c.247-2500A>G		intron_variant		ENST00000304434.11	NP_068586.1
ELOVL5	NM_001242828.2	c.328-2500A>G		intron_variant			NP_001229757.1
ELOVL5	NM_001301856.2	c.247-2500A>G		intron_variant			NP_001288785.1
ELOVL5	NM_001242830.2	c.247-2500A>G		intron_variant			NP_001229759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELOVL5	ENST00000304434.11	c.247-2500A>G		intron_variant		1	NM_021814.5	ENSP00000306640.6

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43466 AN: 151876 Hom.: 7406 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.286 AC: 43517 AN: 151994 Hom.: 7423 Cov.: 32 AF XY: 0.286 AC XY: 21222 AN XY: 74298

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.302

Alfa AF: 0.221 Hom.: 5852

Bravo AF: 0.298

Asia WGS AF: 0.198 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.5
DANN	Benign	0.85

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: rs2281274; hg19: chr6-53143554;