rs9393903

Positions:

• chr6-11042676-G-A

Variant summary

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

The NM_017770.4(ELOVL2):​c.3+1552C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,612 control chromosomes in the GnomAD database, including 3,120 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 0.18 (3120 hom., cov: 30)
• Consequence: ELOVL2 NM_017770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL2	NM_017770.4	c.3+1552C>T		intron_variant		ENST00000354666.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL2	ENST00000354666.4	c.3+1552C>T		intron_variant		1	NM_017770.4	P1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27316 AN: 151494 Hom.: 3115 Cov.: 30

Gnomad AFR AF: 0.0453

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.180 AC: 27321 AN: 151612 Hom.: 3120 Cov.: 30 AF XY: 0.178 AC XY: 13150 AN XY: 74038

Gnomad4 AFR AF: 0.0452

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.240

Alfa AF: 0.229 Hom.: 2463

Bravo AF: 0.183

Asia WGS AF: 0.256 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.93
DANN	Benign	0.67
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: rs9393903; hg19: chr6-11042909;