rs11968589

chr6-53325436-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021814.5(ELOVL5):c.-9+23381G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,122 control chromosomes in the GnomAD database, including 1,311 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1311 hom., cov: 33)
• Consequence: ELOVL5 NM_021814.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL5	NM_021814.5	c.-9+23381G>A		intron_variant		ENST00000304434.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL5	ENST00000304434.11	c.-9+23381G>A		intron_variant		1	NM_021814.5	P1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18827 AN: 152004 Hom.: 1308 Cov.: 33

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0873

Gnomad ASJ AF: 0.0737

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0287

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.124 AC: 18848 AN: 152122 Hom.: 1311 Cov.: 33 AF XY: 0.123 AC XY: 9166 AN XY: 74368

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0871

Gnomad4 ASJ AF: 0.0737

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0291

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.111

Alfa AF: 0.125 Hom.: 166

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
Dann	Benign	0.53

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: rs11968589; hg19: chr6-53190234; COSMIC: COSV58649232;