chr6-11008389-G-C

Variant names:

• chr6-11008389-G-C
• rs3798713
• NM_017770.4:c.67+2357C>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.67+2357C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,074 control chromosomes in the GnomAD database, including 14,160 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 0.42 (14160 hom., cov: 33)
• Consequence: ELOVL2 NM_017770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 45 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL2	NM_017770.4	c.67+2357C>G		intron_variant	Intron 2 of 7	ENST00000354666.4	NP_060240.3
ELOVL2	XM_011514716.4	c.157+2357C>G		intron_variant	Intron 2 of 7		XP_011513018.1
ELOVL2	XM_011514717.4	c.70+2357C>G		intron_variant	Intron 2 of 7		XP_011513019.1
ELOVL2	XM_017010985.2	c.157+2357C>G		intron_variant	Intron 2 of 4		XP_016866474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL2	ENST00000354666.4	c.67+2357C>G		intron_variant	Intron 2 of 7	1	NM_017770.4	ENSP00000346693.3

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63617 AN: 151956 Hom.: 14149 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.419 AC: 63652 AN: 152074 Hom.: 14160 Cov.: 33 AF XY: 0.424 AC XY: 31547 AN XY: 74330

African (AFR) AF: 0.281 AC: 11640 AN: 41482

American (AMR) AF: 0.547 AC: 8357 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1867 AN: 3468

East Asian (EAS) AF: 0.710 AC: 3682 AN: 5186

South Asian (SAS) AF: 0.594 AC: 2860 AN: 4818

European-Finnish (FIN) AF: 0.439 AC: 4635 AN: 10562

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

European-Non Finnish (NFE) AF: 0.430 AC: 29247 AN: 67976

Other (OTH) AF: 0.449 AC: 946 AN: 2106

Alfa AF: 0.444 Hom.: 8599

Bravo AF: 0.417

Asia WGS AF: 0.630 AC: 2189 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.45
PhyloP100		-0.032
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: rs3798713; hg19: chr6-11008622;