chr2-88123239-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001443.3(FABP1):​c.334-135C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 709,064 control chromosomes in the GnomAD database, including 19,880 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 0.17 ( 3041 hom., cov: 33)
Exomes 𝑓: 0.22 ( 16839 hom. )

Consequence

FABP1
NM_001443.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.12
Variant links:
Genes affected
FABP1 (HGNC:3555): (fatty acid binding protein 1) This gene encodes the fatty acid binding protein found in liver. Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. This protein and FABP6 (the ileal fatty acid binding protein) are also able to bind bile acids. It is thought that FABPs roles include fatty acid uptake, transport, and metabolism. [provided by RefSeq, Mar 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FABP1NM_001443.3 linkuse as main transcriptc.334-135C>T intron_variant ENST00000295834.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FABP1ENST00000295834.8 linkuse as main transcriptc.334-135C>T intron_variant 1 NM_001443.3 P1
FABP1ENST00000393750.3 linkuse as main transcriptc.*1213C>T 3_prime_UTR_variant 3/32
FABP1ENST00000495375.1 linkuse as main transcriptn.1874C>T non_coding_transcript_exon_variant 4/43

Frequencies

GnomAD3 genomes
AF:
0.175
AC:
26588
AN:
152048
Hom.:
3036
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0981
Gnomad AMI
AF:
0.147
Gnomad AMR
AF:
0.130
Gnomad ASJ
AF:
0.168
Gnomad EAS
AF:
0.531
Gnomad SAS
AF:
0.468
Gnomad FIN
AF:
0.106
Gnomad MID
AF:
0.212
Gnomad NFE
AF:
0.195
Gnomad OTH
AF:
0.170
GnomAD4 exome
AF:
0.218
AC:
121682
AN:
556898
Hom.:
16839
Cov.:
7
AF XY:
0.228
AC XY:
66600
AN XY:
292082
show subpopulations
Gnomad4 AFR exome
AF:
0.0869
Gnomad4 AMR exome
AF:
0.124
Gnomad4 ASJ exome
AF:
0.157
Gnomad4 EAS exome
AF:
0.508
Gnomad4 SAS exome
AF:
0.443
Gnomad4 FIN exome
AF:
0.122
Gnomad4 NFE exome
AF:
0.191
Gnomad4 OTH exome
AF:
0.206
GnomAD4 genome
AF:
0.175
AC:
26594
AN:
152166
Hom.:
3041
Cov.:
33
AF XY:
0.179
AC XY:
13320
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.0978
Gnomad4 AMR
AF:
0.130
Gnomad4 ASJ
AF:
0.168
Gnomad4 EAS
AF:
0.531
Gnomad4 SAS
AF:
0.468
Gnomad4 FIN
AF:
0.106
Gnomad4 NFE
AF:
0.195
Gnomad4 OTH
AF:
0.177
Alfa
AF:
0.204
Hom.:
1663
Bravo
AF:
0.166
Asia WGS
AF:
0.453
AC:
1572
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.47
DANN
Benign
0.44

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2197076; hg19: chr2-88422758; COSMIC: COSV55558567; COSMIC: COSV55558567; API