rs749540

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_178819.4(GPAT4):​c.*2576G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,086 control chromosomes in the GnomAD database, including 23,366 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 0.55 ( 23366 hom., cov: 33)
Exomes 𝑓: 0.33 ( 0 hom. )

Consequence

GPAT4
NM_178819.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.17

Publications

7 publications found
Variant links:
Genes affected
GPAT4 (HGNC:20880): (glycerol-3-phosphate acyltransferase 4) Lysophosphatidic acid acyltransferases (EC 2.3.1.51) catalyze the conversion of lysophosphatidic acid (LPA) to phosphatidic acid (PA). LPA and PA are involved in signal transduction and lipid biosynthesis.[supplied by OMIM, Apr 2004]

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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GPAT4NM_178819.4 linkc.*2576G>A 3_prime_UTR_variant Exon 13 of 13 ENST00000396987.7 NP_848934.1 Q86UL3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GPAT4ENST00000396987.7 linkc.*2576G>A 3_prime_UTR_variant Exon 13 of 13 1 NM_178819.4 ENSP00000380184.3 Q86UL3

Frequencies

GnomAD3 genomes
AF:
0.548
AC:
83241
AN:
151962
Hom.:
23332
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.644
Gnomad AMI
AF:
0.498
Gnomad AMR
AF:
0.518
Gnomad ASJ
AF:
0.639
Gnomad EAS
AF:
0.469
Gnomad SAS
AF:
0.431
Gnomad FIN
AF:
0.382
Gnomad MID
AF:
0.680
Gnomad NFE
AF:
0.531
Gnomad OTH
AF:
0.580
GnomAD4 exome
AF:
0.333
AC:
2
AN:
6
Hom.:
0
Cov.:
0
AF XY:
0.250
AC XY:
1
AN XY:
4
show subpopulations
African (AFR)
AC:
0
AN:
0
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:
0.500
AC:
1
AN:
2
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.500
AC:
1
AN:
2
Other (OTH)
AF:
0.00
AC:
0
AN:
2
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
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:
0.548
AC:
83325
AN:
152080
Hom.:
23366
Cov.:
33
AF XY:
0.540
AC XY:
40106
AN XY:
74330
show subpopulations
African (AFR)
AF:
0.644
AC:
26719
AN:
41484
American (AMR)
AF:
0.517
AC:
7897
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.639
AC:
2217
AN:
3468
East Asian (EAS)
AF:
0.469
AC:
2422
AN:
5166
South Asian (SAS)
AF:
0.432
AC:
2080
AN:
4810
European-Finnish (FIN)
AF:
0.382
AC:
4048
AN:
10584
Middle Eastern (MID)
AF:
0.680
AC:
200
AN:
294
European-Non Finnish (NFE)
AF:
0.531
AC:
36065
AN:
67980
Other (OTH)
AF:
0.580
AC:
1223
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1914
3828
5741
7655
9569
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
704
1408
2112
2816
3520
<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:
0.389
Hom.:
1015
Bravo
AF:
0.564
Asia WGS
AF:
0.438
AC:
1521
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.33
DANN
Benign
0.58
PhyloP100
-1.2
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: rs749540; hg19: chr8-41481096; API