6-53269306-C-CACAG

Position:

• chr6-53269306-C-CACAG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_021814.5(ELOVL5):​c.757-40_757-37dupCTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 1,531,430 control chromosomes in the GnomAD database, including 190,919 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.58 (28120 hom., cov: 0)
  • Exomes 𝑓: 0.48 (162799 hom.)
• Consequence: ELOVL5 NM_021814.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1 O:1
• Conservation: PhyloP100: 1.79

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 -10 ACMG points.

• BP6: Variant 6-53269306-C-CACAG is Benign according to our data. Variant chr6-53269306-C-CACAG is described in ClinVar as [Benign]. Clinvar id is 218139.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELOVL5	NM_021814.5	c.757-40_757-37dupCTGT		intron_variant		ENST00000304434.11	NP_068586.1
ELOVL5	NM_001242828.2	c.838-40_838-37dupCTGT		intron_variant			NP_001229757.1
ELOVL5	NM_001301856.2	c.757-40_757-37dupCTGT		intron_variant			NP_001288785.1
ELOVL5	NM_001242830.2	c.632-40_632-37dupCTGT		intron_variant			NP_001229759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELOVL5	ENST00000304434.11	c.757-40_757-37dupCTGT		intron_variant		1	NM_021814.5	ENSP00000306640.6
ELOVL5	ENST00000542638.5	c.632-40_632-37dupCTGT		intron_variant		1		ENSP00000440728.2
ELOVL5	ENST00000370918.8	c.838-40_838-37dupCTGT		intron_variant		2		ENSP00000359956.5

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88114 AN: 151464 Hom.: 28060 Cov.: 0

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.587

GnomAD3 exomes AF: 0.491 AC: 95983 AN: 195468 Hom.: 24840 AF XY: 0.480 AC XY: 51292 AN XY: 106868

Gnomad AFR exome AF: 0.866

Gnomad AMR exome AF: 0.563

Gnomad ASJ exome AF: 0.526

Gnomad EAS exome AF: 0.396

Gnomad SAS exome AF: 0.440

Gnomad FIN exome AF: 0.376

Gnomad NFE exome AF: 0.468

Gnomad OTH exome AF: 0.479

GnomAD4 exome AF: 0.478 AC: 659362 AN: 1379846 Hom.: 162799 Cov.: 25 AF XY: 0.476 AC XY: 324236 AN XY: 681652

Gnomad4 AFR exome AF: 0.886

Gnomad4 AMR exome AF: 0.575

Gnomad4 ASJ exome AF: 0.534

Gnomad4 EAS exome AF: 0.367

Gnomad4 SAS exome AF: 0.451

Gnomad4 FIN exome AF: 0.382

Gnomad4 NFE exome AF: 0.471

Gnomad4 OTH exome AF: 0.499

GnomAD4 genome AF: 0.582 AC: 88234 AN: 151584 Hom.: 28120 Cov.: 0 AF XY: 0.573 AC XY: 42461 AN XY: 74052

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.588

Alfa AF: 0.522 Hom.: 3973

Bravo AF: 0.612

Asia WGS AF: 0.467 AC: 1620 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1 Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1 Other:1

Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 25, 2019	- -
not provided, no classification provided	not provided	Institute of Human Genetics, Justus-Liebig University	-	- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3830806; hg19: chr6-53134104;