rs3830806

Variant names:

• chr6-53269306-C-CACAG
• rs3830806
• NM_021814.5:c.757-40_757-37dupCTGT

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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 -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 VariationId 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.

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.757-40_757-37dupCTGT		intron	N/A	NP_068586.1
	ELOVL5	NM_001242828.2		c.838-40_838-37dupCTGT		intron	N/A	NP_001229757.1
	ELOVL5	NM_001301856.2		c.757-40_757-37dupCTGT		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.757-37_757-36insCTGT		intron	N/A	ENSP00000306640.6
	ELOVL5	ENST00000542638.5	TSL:1	c.632-37_632-36insCTGT		intron	N/A	ENSP00000440728.2
	ELOVL5	ENST00000370918.8	TSL:2	c.838-37_838-36insCTGT		intron	N/A	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

GnomAD2 exomes AF: 0.491 AC: 95983 AN: 195468 AF XY: 0.480

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 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

African (AFR) AF: 0.886 AC: 26973 AN: 30456

American (AMR) AF: 0.575 AC: 18951 AN: 32966

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 12320 AN: 23088

East Asian (EAS) AF: 0.367 AC: 13854 AN: 37796

South Asian (SAS) AF: 0.451 AC: 34194 AN: 75888

European-Finnish (FIN) AF: 0.382 AC: 19616 AN: 51390

Middle Eastern (MID) AF: 0.574 AC: 3109 AN: 5414

European-Non Finnish (NFE) AF: 0.471 AC: 502078 AN: 1066244

Other (OTH) AF: 0.499 AC: 28267 AN: 56604

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

African (AFR) AF: 0.868 AC: 35838 AN: 41272

American (AMR) AF: 0.552 AC: 8407 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1899 AN: 3460

East Asian (EAS) AF: 0.413 AC: 2125 AN: 5144

South Asian (SAS) AF: 0.445 AC: 2142 AN: 4814

European-Finnish (FIN) AF: 0.365 AC: 3839 AN: 10506

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32072 AN: 67858

Other (OTH) AF: 0.588 AC: 1241 AN: 2110

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

Sep 25, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Institute of Human Genetics, Justus-Liebig University

Significance: not provided

Review Status: no classification provided

Collection Method: not provided

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3830806; hg19: chr6-53134104;