4-110105771-C-T

Variant summary

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

The NM_024090.3(ELOVL6):c.90-143G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 697,072 control chromosomes in the GnomAD database, including 32,429 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 0.31 (8436 hom., cov: 32)
  • Exomes 𝑓: 0.27 (23993 hom.)
• Consequence: ELOVL6 NM_024090.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

Genes affected

ELOVL6 (HGNC:15829): (ELOVL fatty acid elongase 6) Fatty acid elongases (EC 6.2.1.3), such as ELOVL6, use malonyl-CoA as a 2-carbon donor in the first and rate-limiting step of fatty acid elongation (Moon et al., 2001 [PubMed 11567032]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL6	NM_024090.3	c.90-143G>A		intron_variant		ENST00000302274.8
ELOVL6	NM_001130721.2	c.90-143G>A		intron_variant
ELOVL6	XM_011532233.4	c.90-143G>A		intron_variant
ELOVL6	XM_011532234.4	c.90-143G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL6	ENST00000302274.8	c.90-143G>A		intron_variant		2	NM_024090.3	P1

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47127 AN: 151944 Hom.: 8422 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.281

GnomAD4 exome AF: 0.265 AC: 144539 AN: 545010 Hom.: 23993 AF XY: 0.268 AC XY: 75884 AN XY: 283062

Gnomad4 AFR exome AF: 0.417

Gnomad4 AMR exome AF: 0.323

Gnomad4 ASJ exome AF: 0.253

Gnomad4 EAS exome AF: 0.711

Gnomad4 SAS exome AF: 0.355

Gnomad4 FIN exome AF: 0.317

Gnomad4 NFE exome AF: 0.204

Gnomad4 OTH exome AF: 0.276

GnomAD4 genome AF: 0.310 AC: 47185 AN: 152062 Hom.: 8436 Cov.: 32 AF XY: 0.321 AC XY: 23863 AN XY: 74342

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.281

Alfa AF: 0.245 Hom.: 9761

Bravo AF: 0.314

Asia WGS AF: 0.500 AC: 1737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.8
Dann	Benign	0.37

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: rs10011926; hg19: chr4-111026927; COSMIC: COSV56432625;