Genetic Variant ELOVL6:c.90-143G>A (chr4-110105771-C-T) – 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.90-143G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 697,072 control chromosomes in the GnomAD database, including 32,429 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 0.31 ( 8436 hom., cov: 32)

Exomes 𝑓: 0.27 ( 23993 hom. )

Consequence

ELOVL6
NM_024090.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0110

Publications

11 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ELOVL6	NM_024090.3 link	c.90-143G>A	intron_variant	Intron 1 of 3	ENST00000302274.8	NP_076995.1	Q9H5J4A1LV06
ELOVL6	NM_001130721.2 link	c.90-143G>A	intron_variant	Intron 2 of 4		NP_001124193.1	Q9H5J4A1LV06
ELOVL6	XM_011532233.4 link	c.90-143G>A	intron_variant	Intron 2 of 4		XP_011530535.1	Q9H5J4A1LV06
ELOVL6	XM_011532234.4 link	c.90-143G>A	intron_variant	Intron 2 of 4		XP_011530536.1	Q9H5J4A1LV06

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL6	ENST00000302274.8 link	c.90-143G>A		intron_variant	Intron 1 of 3	2	NM_024090.3	ENSP00000304736.3		Q9H5J4

Frequencies

GnomAD3 genomes

AF:

0.310

AC:

47127

AN:

151944

Hom.:

8422

Cov.:

show subpopulations

Gnomad AFR

AF:

0.413

Gnomad AMI

AF:

0.323

Gnomad AMR

AF:

0.308

Gnomad ASJ

AF:

0.249

Gnomad EAS

AF:

0.709

Gnomad SAS

AF:

0.364

Gnomad FIN

AF:

0.323

Gnomad MID

AF:

0.306

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.281

GnomAD4 exome

AF:

0.265

AC:

144539

AN:

545010

Hom.:

23993

AF XY:

0.268

AC XY:

75884

AN XY:

283062

show subpopulations

African (AFR)

AF:

0.417

AC:

5648

AN:

13550

American (AMR)

AF:

0.323

AC:

5863

AN:

18138

Ashkenazi Jewish (ASJ)

AF:

0.253

AC:

3345

AN:

13232

East Asian (EAS)

AF:

0.711

AC:

20538

AN:

28874

South Asian (SAS)

AF:

0.355

AC:

16443

AN:

46322

European-Finnish (FIN)

AF:

0.317

AC:

10945

AN:

34526

Middle Eastern (MID)

AF:

0.278

AC:

586

AN:

2110

European-Non Finnish (NFE)

AF:

0.204

AC:

73561

AN:

360664

Other (OTH)

AF:

0.276

AC:

7610

AN:

27594

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

4581

9163

13744

18326

22907

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1412

2824

4236

5648

7060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.310

AC:

47185

AN:

152062

Hom.:

8436

Cov.:

AF XY:

0.321

AC XY:

23863

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.413

AC:

17128

AN:

41480

American (AMR)

AF:

0.309

AC:

4722

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.249

AC:

864

AN:

3472

East Asian (EAS)

AF:

0.709

AC:

3659

AN:

5164

South Asian (SAS)

AF:

0.364

AC:

1754

AN:

4824

European-Finnish (FIN)

AF:

0.323

AC:

3403

AN:

10548

Middle Eastern (MID)

AF:

0.305

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.216

AC:

14679

AN:

67976

Other (OTH)

AF:

0.281

AC:

594

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1550

3100

4650

6200

7750

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

470

940

1410

1880

2350

<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:

0.261

Hom.:

17124

Bravo

AF:

0.314

Asia WGS

AF:

0.500

AC:

1737

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.8

(source)

DANN

Benign

0.37

PhyloP100

-0.011

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over