6-11040227-T-C

Variant names:

• chr6-11040227-T-C
• rs13204015
• NM_017770.4:c.3+4001A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_017770.4(ELOVL2):​c.3+4001A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0311 in 152,280 control chromosomes in the GnomAD database, including 116 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 0.031 (116 hom., cov: 32)
• Consequence: ELOVL2 NM_017770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 4 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=-0.57).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0311 (4742/152280) while in subpopulation NFE AF = 0.0511 (3472/68010). AF 95% confidence interval is 0.0496. There are 116 homozygotes in GnomAd4. There are 2212 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 116 AR gene

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.3+4001A>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.3+4001A>G		intron	N/A	ENSP00000346693.3

Frequencies

GnomAD3 genomes AF: 0.0312 AC: 4744 AN: 152162 Hom.: 116 Cov.: 32

Gnomad AFR AF: 0.0108

Gnomad AMI AF: 0.0672

Gnomad AMR AF: 0.0202

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00683

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0511

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0311 AC: 4742 AN: 152280 Hom.: 116 Cov.: 32 AF XY: 0.0297 AC XY: 2212 AN XY: 74472

African (AFR) AF: 0.0107 AC: 446 AN: 41562

American (AMR) AF: 0.0201 AC: 307 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00704 AC: 34 AN: 4828

European-Finnish (FIN) AF: 0.0256 AC: 272 AN: 10620

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0511 AC: 3472 AN: 68010

Other (OTH) AF: 0.0355 AC: 75 AN: 2114

Alfa AF: 0.0433 Hom.: 293

Bravo AF: 0.0306

Asia WGS AF: 0.00404 AC: 14 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	13
DANN	Benign	0.87
PhyloP100		1.0
Mutation Taster		=100/0	polymorphism

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: rs13204015; hg19: chr6-11040460;