Genetic Variant ELOVL6:c.*4825A>T (chr4-110046513-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.536

Publications

1 publications found

Variant links:

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]

ELOVL6 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank	MANE	Protein	UniProt
ELOVL6	NM_024090.3 link	c.*4825A>T	3_prime_UTR_variant	Exon 4 of 4	ENST00000302274.8	NP_076995.1	Q9H5J4A1LV06
ELOVL6	NM_001130721.2 link	c.*4825A>T	3_prime_UTR_variant	Exon 5 of 5		NP_001124193.1	Q9H5J4A1LV06
ELOVL6	XM_011532233.4 link	c.*4825A>T	3_prime_UTR_variant	Exon 5 of 5		XP_011530535.1	Q9H5J4A1LV06
ELOVL6	XM_011532234.4 link	c.*4825A>T	3_prime_UTR_variant	Exon 5 of 5		XP_011530536.1	Q9H5J4A1LV06

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL6	ENST00000302274.8 link	c.*4825A>T		3_prime_UTR_variant	Exon 4 of 4	2	NM_024090.3	ENSP00000304736.3		Q9H5J4
ELOVL6	ENST00000394607.7 link	c.*4825A>T		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000378105.3		Q9H5J4

Frequencies

GnomAD3 genomes

AF:

0.179

AC:

27215

AN:

152008

Hom.:

2981

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.179

AC:

27242

AN:

152126

Hom.:

2985

Cov.:

AF XY:

0.186

AC XY:

13832

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.0920

AC:

3820

AN:

41512

American (AMR)

AF:

0.264

AC:

4031

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

563

AN:

3470

East Asian (EAS)

AF:

0.442

AC:

2287

AN:

5170

South Asian (SAS)

AF:

0.342

AC:

1644

AN:

4812

European-Finnish (FIN)

AF:

0.185

AC:

1951

AN:

10554

Middle Eastern (MID)

AF:

0.224

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.181

AC:

12337

AN:

67998

Other (OTH)

AF:

0.195

AC:

412

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1109

2218

3326

4435

5544

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.46

PhyloP100

-0.54

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over