chr4-110046513-T-A

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

2

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]

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 HGVSp Effect Exon rank MANE Protein UniProt
ELOVL6NM_024090.3 linkc.*4825A>T 3_prime_UTR_variant Exon 4 of 4 ENST00000302274.8 NP_076995.1 Q9H5J4A1LV06
ELOVL6NM_001130721.2 linkc.*4825A>T 3_prime_UTR_variant Exon 5 of 5 NP_001124193.1 Q9H5J4A1LV06
ELOVL6XM_011532233.4 linkc.*4825A>T 3_prime_UTR_variant Exon 5 of 5 XP_011530535.1 Q9H5J4A1LV06
ELOVL6XM_011532234.4 linkc.*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
ELOVL6ENST00000302274.8 linkc.*4825A>T 3_prime_UTR_variant Exon 4 of 4 2 NM_024090.3 ENSP00000304736.3 Q9H5J4
ELOVL6ENST00000394607.7 linkc.*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.:
32
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:
5
AN:
22
Hom.:
1
Cov.:
0
AF XY:
0.250
AC XY:
4
AN XY:
16
show subpopulations
African (AFR)
AF:
0.500
AC:
1
AN:
2
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
2
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.250
AC:
4
AN:
16
Other (OTH)
AF:
0.00
AC:
0
AN:
2
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
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.:
32
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:
66
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
0
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
0
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
DANN
Benign
0.46
PhyloP100
-0.54
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs3813825; hg19: chr4-110967669; API