4-110052509-C-T

Variant names:

• chr4-110052509-C-T
• rs4141123
• NM_024090.3:c.374-747G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024090.3(ELOVL6):​c.374-747G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,094 control chromosomes in the GnomAD database, including 22,459 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 0.50 (22459 hom., cov: 33)
• Consequence: ELOVL6 NM_024090.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL6	NM_024090.3	c.374-747G>A		intron_variant	Intron 3 of 3	ENST00000302274.8	NP_076995.1
ELOVL6	NM_001130721.2	c.374-747G>A		intron_variant	Intron 4 of 4		NP_001124193.1
ELOVL6	XM_011532233.4	c.374-747G>A		intron_variant	Intron 4 of 4		XP_011530535.1
ELOVL6	XM_011532234.4	c.374-747G>A		intron_variant	Intron 4 of 4		XP_011530536.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL6	ENST00000302274.8	c.374-747G>A		intron_variant	Intron 3 of 3	2	NM_024090.3	ENSP00000304736.3

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76114 AN: 151976 Hom.: 22391 Cov.: 33

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.501 AC: 76240 AN: 152094 Hom.: 22459 Cov.: 33 AF XY: 0.508 AC XY: 37774 AN XY: 74358

African (AFR) AF: 0.800 AC: 33208 AN: 41500

American (AMR) AF: 0.560 AC: 8565 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1287 AN: 3464

East Asian (EAS) AF: 0.687 AC: 3552 AN: 5172

South Asian (SAS) AF: 0.459 AC: 2213 AN: 4826

European-Finnish (FIN) AF: 0.388 AC: 4097 AN: 10548

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21894 AN: 67972

Other (OTH) AF: 0.465 AC: 983 AN: 2116

Alfa AF: 0.423 Hom.: 2483

Bravo AF: 0.529

Asia WGS AF: 0.636 AC: 2213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.60
DANN	Benign	0.42
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism (auto)

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: rs4141123; hg19: chr4-110973665;