Genetic Variant ELOVL2:c.*1655C>T (chr6-10982126-G-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_017770.4(ELOVL2):c.*1655C>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 0.174 in 152,080 control chromosomes in the GnomAD database, including 2,896 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 0.17 ( 2895 hom., cov: 32)

Exomes 𝑓: 0.29 ( 1 hom. )

Consequence

ELOVL2
NM_017770.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.585

Publications

24 publications found

Variant links:

Genes affected

ELOVL2 (HGNC:14416): (ELOVL fatty acid elongase 2) Enables fatty acid elongase activity. Involved in fatty acid elongation, polyunsaturated fatty acid and very long-chain fatty acid biosynthetic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ELOVL2 links:

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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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017770.4. 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
	ELOVL2	NM_017770.4	MANE Select	c.*1655C>T		3_prime_UTR	Exon 8 of 8	NP_060240.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ELOVL2	ENST00000354666.4	TSL:1 MANE Select	c.*1655C>T	3_prime_UTR	Exon 8 of 8	ENSP00000346693.3	Q9NXB9
ELOVL2	ENST00000912166.1		c.*1655C>T	3_prime_UTR	Exon 6 of 6	ENSP00000582225.1
ELOVL2	ENST00000854792.1		c.*1655C>T	3_prime_UTR	Exon 5 of 5	ENSP00000524851.1

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26434

AN:

151920

Hom.:

2888

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0440

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.239

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.251

Gnomad SAS

AF:

0.217

Gnomad FIN

AF:

0.108

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.231

GnomAD4 exome

AF:

0.286

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.357

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.200

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.174

AC:

26441

AN:

152038

Hom.:

2895

Cov.:

AF XY:

0.171

AC XY:

12684

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.0438

AC:

1817

AN:

41488

American (AMR)

AF:

0.239

AC:

3649

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.318

AC:

1103

AN:

3468

East Asian (EAS)

AF:

0.251

AC:

1292

AN:

5154

South Asian (SAS)

AF:

0.217

AC:

1044

AN:

4816

European-Finnish (FIN)

AF:

0.108

AC:

1145

AN:

10570

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.231

AC:

15686

AN:

67960

Other (OTH)

AF:

0.236

AC:

497

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1077

2155

3232

4310

5387

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.219

Hom.:

15682

Bravo

AF:

0.177

Asia WGS

AF:

0.236

AC:

824

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.13

(source)

DANN

Benign

0.51

PhyloP100

-0.58

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over