6-11040227-T-C

Position:

• chr6-11040227-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000354666.4(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 ENST00000354666.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

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=-0.57).
• 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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 116 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELOVL2	NM_017770.4	c.3+4001A>G		intron_variant		ENST00000354666.4	NP_060240.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELOVL2	ENST00000354666.4	c.3+4001A>G		intron_variant		1	NM_017770.4	ENSP00000346693	P1

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

Gnomad4 AFR AF: 0.0107

Gnomad4 AMR AF: 0.0201

Gnomad4 ASJ AF: 0.0202

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00704

Gnomad4 FIN AF: 0.0256

Gnomad4 NFE AF: 0.0511

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.0441 Hom.: 243

Bravo AF: 0.0306

Asia WGS AF: 0.00404 AC: 14 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	13
DANN	Benign	0.87

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

Publications

LitVar

Other links and lift over

dbSNP: rs13204015; hg19: chr6-11040460;