6-10994782-G-C

Variant names:

• chr6-10994782-G-C
• rs2236212
• NM_017770.4:c.505+225C>G

Variant summary

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

The NM_017770.4(ELOVL2):​c.505+225C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,034 control chromosomes in the GnomAD database, including 13,206 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 0.40 (13206 hom., cov: 31)
• Consequence: ELOVL2 NM_017770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394
• Publications: 59 publications found

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

Our verdict: Benign. The variant received -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 = 0.691 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017770.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL2	NM_017770.4	MANE Select	c.505+225C>G		intron	N/A	NP_060240.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL2	ENST00000354666.4	TSL:1 MANE Select	c.505+225C>G		intron	N/A	ENSP00000346693.3

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60292 AN: 151916 Hom.: 13191 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.397 AC: 60328 AN: 152034 Hom.: 13206 Cov.: 31 AF XY: 0.403 AC XY: 29976 AN XY: 74312

African (AFR) AF: 0.219 AC: 9069 AN: 41472

American (AMR) AF: 0.539 AC: 8239 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1865 AN: 3468

East Asian (EAS) AF: 0.710 AC: 3664 AN: 5162

South Asian (SAS) AF: 0.591 AC: 2845 AN: 4812

European-Finnish (FIN) AF: 0.428 AC: 4525 AN: 10562

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28794 AN: 67958

Other (OTH) AF: 0.430 AC: 909 AN: 2112

Alfa AF: 0.435 Hom.: 8347

Bravo AF: 0.393

Asia WGS AF: 0.627 AC: 2181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.58
DANN	Benign	0.65
PhyloP100		-0.39
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: rs2236212; hg19: chr6-10995015;