4-110057342-A-G

Variant names:

• chr4-110057342-A-G
• rs1557803
• NM_024090.3:c.373+2261T>C

Variant summary

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

The NM_024090.3(ELOVL6):​c.373+2261T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,524 control chromosomes in the GnomAD database, including 22,413 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 (22413 hom., cov: 29)
• Consequence: ELOVL6 NM_024090.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 6 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024090.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL6	NM_024090.3	MANE Select	c.373+2261T>C		intron	N/A	NP_076995.1
	ELOVL6	NM_001130721.2		c.373+2261T>C		intron	N/A	NP_001124193.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL6	ENST00000302274.8	TSL:2 MANE Select	c.373+2261T>C		intron	N/A	ENSP00000304736.3
	ELOVL6	ENST00000394607.7	TSL:1	c.373+2261T>C		intron	N/A	ENSP00000378105.3
	ELOVL6	ENST00000506625.5	TSL:4	c.373+2261T>C		intron	N/A	ENSP00000425488.1

Frequencies

GnomAD3 genomes AF: 0.501 AC: 75909 AN: 151406 Hom.: 22345 Cov.: 29

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.502 AC: 76035 AN: 151524 Hom.: 22413 Cov.: 29 AF XY: 0.509 AC XY: 37641 AN XY: 74014

African (AFR) AF: 0.800 AC: 33023 AN: 41276

American (AMR) AF: 0.567 AC: 8632 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1316 AN: 3466

East Asian (EAS) AF: 0.684 AC: 3500 AN: 5114

South Asian (SAS) AF: 0.458 AC: 2198 AN: 4796

European-Finnish (FIN) AF: 0.389 AC: 4068 AN: 10448

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

European-Non Finnish (NFE) AF: 0.322 AC: 21874 AN: 67876

Other (OTH) AF: 0.466 AC: 982 AN: 2106

Alfa AF: 0.370 Hom.: 19211

Bravo AF: 0.531

Asia WGS AF: 0.637 AC: 2216 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.36
PhyloP100		-1.8
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: rs1557803; hg19: chr4-110978498;