6-53335501-C-G

Variant names:

• chr6-53335501-C-G
• rs2397142
• NM_021814.5:c.-9+13316G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021814.5(ELOVL5):​c.-9+13316G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,008 control chromosomes in the GnomAD database, including 11,148 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 0.36 (11148 hom., cov: 32)
• Consequence: ELOVL5 NM_021814.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 14 publications found

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]

RPS16P5 (HGNC:36183): (ribosomal protein S16 pseudogene 5)

ENSG00000296291 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021814.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL5	NM_021814.5	MANE Select	c.-9+13316G>C		intron	N/A	NP_068586.1	Q9NYP7-1
	ELOVL5	NM_001242828.2		c.-9+13316G>C		intron	N/A	NP_001229757.1	Q9NYP7-2
	ELOVL5	NM_001301856.2		c.-9+12849G>C		intron	N/A	NP_001288785.1	Q9NYP7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL5	ENST00000304434.11	TSL:1 MANE Select	c.-9+13316G>C		intron	N/A	ENSP00000306640.6	Q9NYP7-1
	ELOVL5	ENST00000542638.5	TSL:1	c.-9+13316G>C		intron	N/A	ENSP00000440728.2	A0A0A0MTI6
	ELOVL5	ENST00000370913.5	TSL:1	c.-9+13316G>C		intron	N/A	ENSP00000359951.5	Q9NYP7-3

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55188 AN: 151890 Hom.: 11142 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.363 AC: 55232 AN: 152008 Hom.: 11148 Cov.: 32 AF XY: 0.356 AC XY: 26453 AN XY: 74304

African (AFR) AF: 0.553 AC: 22898 AN: 41414

American (AMR) AF: 0.238 AC: 3640 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1432 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1910 AN: 5166

South Asian (SAS) AF: 0.386 AC: 1859 AN: 4820

European-Finnish (FIN) AF: 0.219 AC: 2321 AN: 10576

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20061 AN: 67978

Other (OTH) AF: 0.364 AC: 768 AN: 2110

Alfa AF: 0.324 Hom.: 1163

Bravo AF: 0.371

Asia WGS AF: 0.379 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.5
DANN	Benign	0.43
PhyloP100		-0.031
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2397142; hg19: chr6-53200299;