rs953413

chr6-11012626-G-Achr6-11012626-G-C

Variant summary

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

The NM_017770.4(ELOVL2):c.4-1817C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,084 control chromosomes in the GnomAD database, including 24,091 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 0.55 (24091 hom., cov: 33)
• Consequence: ELOVL2 NM_017770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

Genes affected

ELOVL2 (HGNC:14416): (ELOVL fatty acid elongase 2) Enables fatty acid elongase activity. Involved in fatty acid elongation, polyunsaturated fatty acid and very long-chain fatty acid biosynthetic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL2	NM_017770.4	c.4-1817C>T		intron_variant		ENST00000354666.4
ELOVL2	XM_011514716.4	c.-649C>T		5_prime_UTR_variant	1/8
ELOVL2	XM_011514717.4	c.-139C>T		5_prime_UTR_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL2	ENST00000354666.4	c.4-1817C>T		intron_variant		1	NM_017770.4	P1

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83269 AN: 151966 Hom.: 24041 Cov.: 33

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.548 AC: 83376 AN: 152084 Hom.: 24091 Cov.: 33 AF XY: 0.554 AC XY: 41215 AN XY: 74338

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.542

Alfa AF: 0.445 Hom.: 6518

Bravo AF: 0.565

Asia WGS AF: 0.754 AC: 2619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.28
Dann	Benign	0.85
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs953413; hg19: chr6-11012859;