6-53269366-C-CCTTTT

Variant summary

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

The NM_021814.5(ELOVL5):c.757-97_757-96insAAAAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 959,832 control chromosomes in the GnomAD database, including 71,061 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.44 (16291 hom., cov: 0)
  • Exomes 𝑓: 0.36 (54770 hom.)
• Consequence: ELOVL5 NM_021814.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.474

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 6-53269366-C-CCTTTT is Benign according to our data. Variant chr6-53269366-C-CCTTTT is described in ClinVar as [Benign]. Clinvar id is 1248305.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL5	NM_021814.5	c.757-97_757-96insAAAAG		intron_variant		ENST00000304434.11
ELOVL5	NM_001242828.2	c.838-97_838-96insAAAAG		intron_variant
ELOVL5	NM_001242830.2	c.632-97_632-96insAAAAG		intron_variant
ELOVL5	NM_001301856.2	c.757-97_757-96insAAAAG		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL5	ENST00000304434.11	c.757-97_757-96insAAAAG		intron_variant		1	NM_021814.5	P1
ELOVL5	ENST00000542638.5	c.632-97_632-96insAAAAG		intron_variant		1
ELOVL5	ENST00000370918.8	c.838-97_838-96insAAAAG		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67277 AN: 151582 Hom.: 16263 Cov.: 0

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.467

GnomAD4 exome AF: 0.358 AC: 289456 AN: 808136 Hom.: 54770 AF XY: 0.358 AC XY: 144099 AN XY: 402946

Gnomad4 AFR exome AF: 0.645

Gnomad4 AMR exome AF: 0.473

Gnomad4 ASJ exome AF: 0.460

Gnomad4 EAS exome AF: 0.348

Gnomad4 SAS exome AF: 0.388

Gnomad4 FIN exome AF: 0.244

Gnomad4 NFE exome AF: 0.348

Gnomad4 OTH exome AF: 0.389

GnomAD4 genome AF: 0.444 AC: 67360 AN: 151696 Hom.: 16291 Cov.: 0 AF XY: 0.437 AC XY: 32364 AN XY: 74130

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.469

Alfa AF: 0.171 Hom.: 238

Bravo AF: 0.473

Asia WGS AF: 0.434 AC: 1507 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

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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: rs70980834; hg19: chr6-53134164;