NM_001442.3:c.73+628C>T

Variant summary

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

The NM_001442.3(FABP4):​c.73+628C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,018 control chromosomes in the GnomAD database, including 15,351 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 0.40 ( 15351 hom., cov: 32)

Consequence

FABP4
NM_001442.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.88

Publications

7 publications found
Variant links:
Genes affected
FABP4 (HGNC:3559): (fatty acid binding protein 4) FABP4 encodes the fatty acid binding protein found in adipocytes. Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. It is thought that FABPs roles include fatty acid uptake, transport, and metabolism. [provided by RefSeq, Jul 2008]
FABP4 Gene-Disease associations (from GenCC):
  • schizophrenia
    Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FABP4NM_001442.3 linkc.73+628C>T intron_variant Intron 1 of 3 ENST00000256104.5 NP_001433.1 P15090E7DVW4
LOC101927118XR_001745980.2 linkn.517+20493G>A intron_variant Intron 1 of 8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FABP4ENST00000256104.5 linkc.73+628C>T intron_variant Intron 1 of 3 1 NM_001442.3 ENSP00000256104.4 P15090

Frequencies

GnomAD3 genomes
AF:
0.404
AC:
61334
AN:
151898
Hom.:
15302
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.683
Gnomad AMI
AF:
0.105
Gnomad AMR
AF:
0.359
Gnomad ASJ
AF:
0.269
Gnomad EAS
AF:
0.744
Gnomad SAS
AF:
0.298
Gnomad FIN
AF:
0.200
Gnomad MID
AF:
0.288
Gnomad NFE
AF:
0.269
Gnomad OTH
AF:
0.375
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.404
AC:
61444
AN:
152018
Hom.:
15351
Cov.:
32
AF XY:
0.400
AC XY:
29693
AN XY:
74306
show subpopulations
African (AFR)
AF:
0.684
AC:
28360
AN:
41462
American (AMR)
AF:
0.359
AC:
5477
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
0.269
AC:
931
AN:
3464
East Asian (EAS)
AF:
0.743
AC:
3845
AN:
5174
South Asian (SAS)
AF:
0.299
AC:
1444
AN:
4822
European-Finnish (FIN)
AF:
0.200
AC:
2115
AN:
10580
Middle Eastern (MID)
AF:
0.279
AC:
82
AN:
294
European-Non Finnish (NFE)
AF:
0.269
AC:
18299
AN:
67940
Other (OTH)
AF:
0.377
AC:
795
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1613
3226
4839
6452
8065
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
546
1092
1638
2184
2730
<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:
0.362
Hom.:
1574
Bravo
AF:
0.433
Asia WGS
AF:
0.515
AC:
1790
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.053
DANN
Benign
0.51
PhyloP100
-1.9
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: rs2290201; hg19: chr8-82394702; API