dbSNP rs12195587: ELOVL2:p.Tyr253Tyr (chr6-10989709-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_017770.4(ELOVL2):c.759C>T(p.Tyr253Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,611,924 control chromosomes in the GnomAD database, including 20,554 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 0.11 ( 1224 hom., cov: 33)

Exomes 𝑓: 0.15 ( 19330 hom. )

Consequence

ELOVL2
NM_017770.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.136

Publications

14 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP7

Synonymous conserved (PhyloP=0.136 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
ELOVL2	NM_017770.4 link	c.759C>T	p.Tyr253Tyr	synonymous_variant	Exon 7 of 8	ENST00000354666.4	NP_060240.3
ELOVL2	XM_011514716.4 link	c.849C>T	p.Tyr283Tyr	synonymous_variant	Exon 7 of 8		XP_011513018.1
ELOVL2	XM_011514717.4 link	c.762C>T	p.Tyr254Tyr	synonymous_variant	Exon 7 of 8		XP_011513019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL2	ENST00000354666.4 link	c.759C>T	p.Tyr253Tyr	synonymous_variant	Exon 7 of 8	1	NM_017770.4	ENSP00000346693.3

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16644

AN:

151918

Hom.:

1225

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0321

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.0804

Gnomad ASJ

AF:

0.0683

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.0826

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.0951

GnomAD2 exomes

AF:

0.117

AC:

29344

AN:

251236

AF XY:

0.120

show subpopulations

Gnomad AFR exome

AF:

0.0284

Gnomad AMR exome

AF:

0.0648

Gnomad ASJ exome

AF:

0.0819

Gnomad EAS exome

AF:

0.000326

Gnomad FIN exome

AF:

0.131

Gnomad NFE exome

AF:

0.170

Gnomad OTH exome

AF:

0.122

GnomAD4 exome

AF:

0.155

AC:

225639

AN:

1459900

Hom.:

19330

Cov.:

AF XY:

0.153

AC XY:

111255

AN XY:

726334

show subpopulations

African (AFR)

AF:

0.0247

AC:

827

AN:

33466

American (AMR)

AF:

0.0671

AC:

3000

AN:

44704

Ashkenazi Jewish (ASJ)

AF:

0.0771

AC:

2015

AN:

26120

East Asian (EAS)

AF:

0.000277

AC:

AN:

39690

South Asian (SAS)

AF:

0.0984

AC:

8483

AN:

86214

European-Finnish (FIN)

AF:

0.131

AC:

7013

AN:

53410

Middle Eastern (MID)

AF:

0.0702

AC:

405

AN:

5768

European-Non Finnish (NFE)

AF:

0.177

AC:

196230

AN:

1110198

Other (OTH)

AF:

0.127

AC:

7655

AN:

60330

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

8294

16587

24881

33174

41468

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6716

13432

20148

26864

33580

<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:

0.109

AC:

16638

AN:

152024

Hom.:

1224

Cov.:

AF XY:

0.107

AC XY:

7921

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.0321

AC:

1331

AN:

41456

American (AMR)

AF:

0.0802

AC:

1225

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0683

AC:

237

AN:

3468

East Asian (EAS)

AF:

0.00232

AC:

AN:

5182

South Asian (SAS)

AF:

0.0827

AC:

398

AN:

4812

European-Finnish (FIN)

AF:

0.136

AC:

1434

AN:

10530

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.171

AC:

11627

AN:

67990

Other (OTH)

AF:

0.0937

AC:

198

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

754

1507

2261

3014

3768

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

200

400

600

800

1000

<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:

0.138

Hom.:

2781

Bravo

AF:

0.102

Asia WGS

AF:

0.0320

AC:

112

AN:

3478

EpiCase

AF:

0.155

EpiControl

AF:

0.152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.3

(source)

DANN

Benign

0.32

PhyloP100

0.14

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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