chr4-110156005-C-T

Variant names:

• chr4-110156005-C-T
• rs7694475
• NM_024090.3:c.89+42242G>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.89+42242G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,186 control chromosomes in the GnomAD database, including 46,695 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 0.78 (46695 hom., cov: 33)
• Consequence: ELOVL6 NM_024090.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL6	NM_024090.3	MANE Select	c.89+42242G>A		intron	N/A	NP_076995.1	Q9H5J4
	ELOVL6	NM_001130721.2		c.89+42242G>A		intron	N/A	NP_001124193.1	Q9H5J4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL6	ENST00000302274.8	TSL:2 MANE Select	c.89+42242G>A		intron	N/A	ENSP00000304736.3	Q9H5J4
	ELOVL6	ENST00000394607.7	TSL:1	c.89+42242G>A		intron	N/A	ENSP00000378105.3	Q9H5J4
	ELOVL6	ENST00000907637.1		c.89+42242G>A		intron	N/A	ENSP00000577696.1

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118750 AN: 152068 Hom.: 46657 Cov.: 33

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.781 AC: 118845 AN: 152186 Hom.: 46695 Cov.: 33 AF XY: 0.781 AC XY: 58137 AN XY: 74418

African (AFR) AF: 0.851 AC: 35355 AN: 41534

American (AMR) AF: 0.752 AC: 11494 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2627 AN: 3472

East Asian (EAS) AF: 0.836 AC: 4333 AN: 5180

South Asian (SAS) AF: 0.639 AC: 3079 AN: 4818

European-Finnish (FIN) AF: 0.779 AC: 8242 AN: 10578

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51177 AN: 68000

Other (OTH) AF: 0.768 AC: 1621 AN: 2110

Alfa AF: 0.750 Hom.: 22057

Bravo AF: 0.784

Asia WGS AF: 0.729 AC: 2530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.17
DANN	Benign	0.72
PhyloP100		-1.4
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: rs7694475; hg19: chr4-111077161;