6-11035739-T-C

Position:

• chr6-11035739-T-C

Variant summary

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

The NM_017770.4(ELOVL2):​c.3+8489A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,188 control chromosomes in the GnomAD database, including 9,374 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 0.30 (9374 hom., cov: 33)
• Consequence: ELOVL2 NM_017770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL2	NM_017770.4	c.3+8489A>G		intron_variant		ENST00000354666.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL2	ENST00000354666.4	c.3+8489A>G		intron_variant		1	NM_017770.4	P1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45070 AN: 152070 Hom.: 9348 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.297 AC: 45151 AN: 152188 Hom.: 9374 Cov.: 33 AF XY: 0.292 AC XY: 21706 AN XY: 74430

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.240

Alfa AF: 0.237 Hom.: 2636

Bravo AF: 0.317

Asia WGS AF: 0.174 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.54
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs6936315; hg19: chr6-11035972;