Genetic Variant NM_017770.4:c.174C>T (chr6-11005453-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_017770.4(ELOVL2):c.174C>T(p.Asn58Asn) variant causes a synonymous change. The variant allele was found at a frequency of 0.226 in 1,613,114 control chromosomes in the GnomAD database, including 42,253 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 0.21 ( 3444 hom., cov: 32)

Exomes 𝑓: 0.23 ( 38809 hom. )

Consequence

ELOVL2
NM_017770.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.68

Publications

20 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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL2	NM_017770.4 link	c.174C>T	p.Asn58Asn	synonymous_variant	Exon 3 of 8	ENST00000354666.4	NP_060240.3	Q9NXB9A0A024QZV3
ELOVL2	XM_011514716.4 link	c.264C>T	p.Asn88Asn	synonymous_variant	Exon 3 of 8		XP_011513018.1
ELOVL2	XM_011514717.4 link	c.177C>T	p.Asn59Asn	synonymous_variant	Exon 3 of 8		XP_011513019.1
ELOVL2	XM_017010985.2 link	c.264C>T	p.Asn88Asn	synonymous_variant	Exon 3 of 5		XP_016866474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL2	ENST00000354666.4 link	c.174C>T	p.Asn58Asn	synonymous_variant	Exon 3 of 8	1	NM_017770.4	ENSP00000346693.3		Q9NXB9

Frequencies

GnomAD3 genomes

AF:

0.209

AC:

31824

AN:

151970

Hom.:

3438

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.192

Gnomad AMR

AF:

0.255

Gnomad ASJ

AF:

0.317

Gnomad EAS

AF:

0.268

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.108

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.256

GnomAD2 exomes

AF:

0.221

AC:

55360

AN:

251036

AF XY:

0.223

show subpopulations

Gnomad AFR exome

AF:

0.163

Gnomad AMR exome

AF:

0.224

Gnomad ASJ exome

AF:

0.313

Gnomad EAS exome

AF:

0.278

Gnomad FIN exome

AF:

0.114

Gnomad NFE exome

AF:

0.229

Gnomad OTH exome

AF:

0.230

GnomAD4 exome

AF:

0.228

AC:

332967

AN:

1461026

Hom.:

38809

Cov.:

AF XY:

0.228

AC XY:

165838

AN XY:

726846

show subpopulations

African (AFR)

AF:

0.157

AC:

5266

AN:

33450

American (AMR)

AF:

0.230

AC:

10277

AN:

44668

Ashkenazi Jewish (ASJ)

AF:

0.317

AC:

8268

AN:

26116

East Asian (EAS)

AF:

0.269

AC:

10662

AN:

39678

South Asian (SAS)

AF:

0.224

AC:

19292

AN:

86164

European-Finnish (FIN)

AF:

0.119

AC:

6358

AN:

53410

Middle Eastern (MID)

AF:

0.288

AC:

1661

AN:

5766

European-Non Finnish (NFE)

AF:

0.231

AC:

256447

AN:

1111394

Other (OTH)

AF:

0.244

AC:

14736

AN:

60380

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.457

Heterozygous variant carriers

12913

25825

38738

51650

64563

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8770

17540

26310

35080

43850

<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:

0.209

AC:

31850

AN:

152088

Hom.:

3444

Cov.:

AF XY:

0.205

AC XY:

15223

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.161

AC:

6680

AN:

41502

American (AMR)

AF:

0.255

AC:

3895

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.317

AC:

1101

AN:

3468

East Asian (EAS)

AF:

0.267

AC:

1379

AN:

5160

South Asian (SAS)

AF:

0.228

AC:

1098

AN:

4806

European-Finnish (FIN)

AF:

0.108

AC:

1147

AN:

10588

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.231

AC:

15733

AN:

67974

Other (OTH)

AF:

0.261

AC:

551

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1279

2558

3838

5117

6396

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

332

664

996

1328

1660

<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:

0.222

Hom.:

3885

Bravo

AF:

0.217

Asia WGS

AF:

0.265

AC:

925

AN:

3478

EpiCase

AF:

0.240

EpiControl

AF:

0.244

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

9.3

(source)

DANN

Benign

0.62

PhyloP100

3.7

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