6-53269503-A-G

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.757-233T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,924 control chromosomes in the GnomAD database, including 10,937 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.36 (10937 hom., cov: 31)
• Consequence: ELOVL5 NM_021814.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.205

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=-0.88).
• BP6: Variant 6-53269503-A-G is Benign according to our data. Variant chr6-53269503-A-G is described in ClinVar as [Benign]. Clinvar id is 1293375.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL5	NM_021814.5	c.757-233T>C		intron_variant		ENST00000304434.11
ELOVL5	NM_001242828.2	c.838-233T>C		intron_variant
ELOVL5	NM_001242830.2	c.632-233T>C		intron_variant
ELOVL5	NM_001301856.2	c.757-233T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL5	ENST00000304434.11	c.757-233T>C		intron_variant		1	NM_021814.5	P1
ELOVL5	ENST00000542638.5	c.632-233T>C		intron_variant		1
ELOVL5	ENST00000370918.8	c.838-233T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54515 AN: 151806 Hom.: 10934 Cov.: 31

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.359 AC: 54555 AN: 151924 Hom.: 10937 Cov.: 31 AF XY: 0.352 AC XY: 26126 AN XY: 74238

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.363

Alfa AF: 0.320 Hom.: 1073

Bravo AF: 0.367

Asia WGS AF: 0.376 AC: 1308 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

Jun 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.1
Dann	Benign	0.61

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: rs8714; hg19: chr6-53134301;