6-53269450-C-CT

Position:

• chr6-53269450-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_021814.5(ELOVL5):​c.757-181_757-180insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0142 in 147,294 control chromosomes in the GnomAD database, including 39 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.014 (39 hom., cov: 32)
• Consequence: ELOVL5 NM_021814.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.381

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 6-53269450-C-CT is Benign according to our data. Variant chr6-53269450-C-CT is described in ClinVar as [Likely_benign]. Clinvar id is 1321663.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0142 (2091/147294) while in subpopulation AFR AF= 0.0403 (1629/40464). AF 95% confidence interval is 0.0386. There are 39 homozygotes in gnomad4. There are 995 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 2091 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL5	NM_021814.5	c.757-181_757-180insA		intron_variant		ENST00000304434.11
ELOVL5	NM_001242828.2	c.838-181_838-180insA		intron_variant
ELOVL5	NM_001242830.2	c.632-181_632-180insA		intron_variant
ELOVL5	NM_001301856.2	c.757-181_757-180insA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL5	ENST00000304434.11	c.757-181_757-180insA		intron_variant		1	NM_021814.5	P1
ELOVL5	ENST00000542638.5	c.632-181_632-180insA		intron_variant		1
ELOVL5	ENST00000370918.8	c.838-181_838-180insA		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0142 AC: 2084 AN: 147240 Hom.: 39 Cov.: 32

Gnomad AFR AF: 0.0401

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00626

Gnomad ASJ AF: 0.000588

Gnomad EAS AF: 0.000197

Gnomad SAS AF: 0.00277

Gnomad FIN AF: 0.00137

Gnomad MID AF: 0.0229

Gnomad NFE AF: 0.00469

Gnomad OTH AF: 0.0121

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

GnomAD4 genome AF: 0.0142 AC: 2091 AN: 147294 Hom.: 39 Cov.: 32 AF XY: 0.0139 AC XY: 995 AN XY: 71762

Gnomad4 AFR AF: 0.0403

Gnomad4 AMR AF: 0.00625

Gnomad4 ASJ AF: 0.000588

Gnomad4 EAS AF: 0.000197

Gnomad4 SAS AF: 0.00278

Gnomad4 FIN AF: 0.00137

Gnomad4 NFE AF: 0.00469

Gnomad4 OTH AF: 0.0120

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

May 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs3215545; hg19: chr6-53134248;