6-53294778-T-C

Position:

• chr6-53294778-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_021814.5(ELOVL5):​c.58+864A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0623 in 152,248 control chromosomes in the GnomAD database, including 597 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.062 (597 hom., cov: 32)
• Consequence: ELOVL5 NM_021814.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.452

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 6-53294778-T-C is Benign according to our data. Variant chr6-53294778-T-C is described in ClinVar as [Benign]. Clinvar id is 1248645.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL5	NM_021814.5	c.58+864A>G		intron_variant		ENST00000304434.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL5	ENST00000304434.11	c.58+864A>G		intron_variant		1	NM_021814.5	P1

Frequencies

GnomAD3 genomes AF: 0.0623 AC: 9479 AN: 152130 Hom.: 590 Cov.: 32

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.0456

Gnomad SAS AF: 0.0342

Gnomad FIN AF: 0.0195

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.0906

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

GnomAD4 genome AF: 0.0623 AC: 9491 AN: 152248 Hom.: 597 Cov.: 32 AF XY: 0.0628 AC XY: 4673 AN XY: 74448

Gnomad4 AFR AF: 0.0156

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.0457

Gnomad4 SAS AF: 0.0346

Gnomad4 FIN AF: 0.0195

Gnomad4 NFE AF: 0.0633

Gnomad4 OTH AF: 0.0892

Alfa AF: 0.0872 Hom.: 172

Bravo AF: 0.0802

Asia WGS AF: 0.0480 AC: 166 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 25, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.71

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: rs2294859; hg19: chr6-53159576;