rs749540
Variant names:
Your query was ambiguous. Multiple possible variants found:
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
NM_178819.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.17
Publications
7 publications found
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]
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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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.548 AC: 83241AN: 151962Hom.: 23332 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
83241
AN:
151962
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.333 AC: 2AN: 6Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1AN XY: 4 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
6
Hom.:
Cov.:
0
AF XY:
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:
AC:
1
AN:
2
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
1
AN:
2
Other (OTH)
AF:
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: 83325AN: 152080Hom.: 23366 Cov.: 33 AF XY: 0.540 AC XY: 40106AN XY: 74330 show subpopulations
GnomAD4 genome
AF:
AC:
83325
AN:
152080
Hom.:
Cov.:
33
AF XY:
AC XY:
40106
AN XY:
74330
show subpopulations
African (AFR)
AF:
AC:
26719
AN:
41484
American (AMR)
AF:
AC:
7897
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
2217
AN:
3468
East Asian (EAS)
AF:
AC:
2422
AN:
5166
South Asian (SAS)
AF:
AC:
2080
AN:
4810
European-Finnish (FIN)
AF:
AC:
4048
AN:
10584
Middle Eastern (MID)
AF:
AC:
200
AN:
294
European-Non Finnish (NFE)
AF:
AC:
36065
AN:
67980
Other (OTH)
AF:
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
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1521
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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