rs3813825

Positions:

• chr4-110046513-T-A
• chr4-110046513-T-C

Variant summary

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

The NM_024090.3(ELOVL6):​c.*4825A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,148 control chromosomes in the GnomAD database, including 2,986 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 0.18 (2985 hom., cov: 32)
  • Exomes 𝑓: 0.23 (1 hom.)
• Consequence: ELOVL6 NM_024090.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELOVL6	NM_024090.3	c.*4825A>T		3_prime_UTR_variant	4/4	ENST00000302274.8	NP_076995.1
ELOVL6	NM_001130721.2	c.*4825A>T		3_prime_UTR_variant	5/5		NP_001124193.1
ELOVL6	XM_011532233.4	c.*4825A>T		3_prime_UTR_variant	5/5		XP_011530535.1
ELOVL6	XM_011532234.4	c.*4825A>T		3_prime_UTR_variant	5/5		XP_011530536.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELOVL6	ENST00000302274.8	c.*4825A>T		3_prime_UTR_variant	4/4	2	NM_024090.3	ENSP00000304736	P1
ELOVL6	ENST00000394607.7	c.*4825A>T		3_prime_UTR_variant	5/5	1		ENSP00000378105	P1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27215 AN: 152008 Hom.: 2981 Cov.: 32

Gnomad AFR AF: 0.0920

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.192

GnomAD4 exome AF: 0.227 AC: 5 AN: 22 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 4 AN XY: 16

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.179 AC: 27242 AN: 152126 Hom.: 2985 Cov.: 32 AF XY: 0.186 AC XY: 13832 AN XY: 74356

Gnomad4 AFR AF: 0.0920

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.195

Alfa AF: 0.191 Hom.: 392

Bravo AF: 0.181

Asia WGS AF: 0.403 AC: 1396 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.9
DANN	Benign	0.46

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: rs3813825; hg19: chr4-110967669;