rs1799883

Variant names:

• chr4-119320747-T-C
• rs1799883
• NM_000134.4:c.163A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-119320747-T-C
• chr4-119320747-T-A
• chr4-119320747-T-G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000134.4(FABP2):​c.163A>G​(p.Thr55Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 1,604,502 control chromosomes in the GnomAD database, including 433,114 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.74 (41568 hom., cov: 33)
  • Exomes 𝑓: 0.73 (391546 hom.)
• Consequence: FABP2 NM_000134.4 missense
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.413
• Publications: 287 publications found

Genes affected

FABP2 (HGNC:3556): (fatty acid binding protein 2) The protein encoded by this gene is an intracellular fatty acid-binding protein that participates in the uptake, intracellular metabolism, and transport of long-chain fatty acids. The encoded protein is also involved in the modulation of cell growth and proliferation. This protein binds saturated long-chain fatty acids with high affinity, and may act as a lipid sensor to maintain energy homeostasis. [provided by RefSeq, Aug 2017]

ENSG00000294020 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=1.4492882E-6).
• BP6: Variant 4-119320747-T-C is Benign according to our data. Variant chr4-119320747-T-C is described in ClinVar as Benign. ClinVar VariationId is 16494.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000134.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP2	NM_000134.4	MANE Select	c.163A>G	p.Thr55Ala	missense	Exon 2 of 4	NP_000125.2	P12104

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP2	ENST00000274024.4	TSL:1 MANE Select	c.163A>G	p.Thr55Ala	missense	Exon 2 of 4	ENSP00000274024.3	P12104
	ENSG00000294020	ENST00000720595.1		n.176-13581T>C		intron	N/A
	ENSG00000294020	ENST00000720596.1		n.224-13581T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112240 AN: 151834 Hom.: 41517 Cov.: 33

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.751

GnomAD2 exomes AF: 0.726 AC: 176270 AN: 242864 AF XY: 0.721

Gnomad AFR exome AF: 0.770

Gnomad AMR exome AF: 0.733

Gnomad ASJ exome AF: 0.744

Gnomad EAS exome AF: 0.737

Gnomad FIN exome AF: 0.722

Gnomad NFE exome AF: 0.729

Gnomad OTH exome AF: 0.718

GnomAD4 exome AF: 0.734 AC: 1065485 AN: 1452550 Hom.: 391546 Cov.: 38 AF XY: 0.731 AC XY: 527879 AN XY: 722600

African (AFR) AF: 0.765 AC: 25111 AN: 32826

American (AMR) AF: 0.735 AC: 31614 AN: 43036

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 19304 AN: 25976

East Asian (EAS) AF: 0.684 AC: 26822 AN: 39204

South Asian (SAS) AF: 0.676 AC: 57194 AN: 84616

European-Finnish (FIN) AF: 0.720 AC: 38235 AN: 53082

Middle Eastern (MID) AF: 0.722 AC: 4116 AN: 5698

European-Non Finnish (NFE) AF: 0.739 AC: 818691 AN: 1108114

Other (OTH) AF: 0.740 AC: 44398 AN: 59998

GnomAD4 genome AF: 0.739 AC: 112356 AN: 151952 Hom.: 41568 Cov.: 33 AF XY: 0.735 AC XY: 54544 AN XY: 74260

African (AFR) AF: 0.771 AC: 31961 AN: 41474

American (AMR) AF: 0.719 AC: 10966 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2532 AN: 3470

East Asian (EAS) AF: 0.724 AC: 3733 AN: 5156

South Asian (SAS) AF: 0.682 AC: 3289 AN: 4824

European-Finnish (FIN) AF: 0.716 AC: 7568 AN: 10570

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50010 AN: 67900

Other (OTH) AF: 0.753 AC: 1587 AN: 2108

Alfa AF: 0.737 Hom.: 114164

Bravo AF: 0.746

TwinsUK AF: 0.725 AC: 2688

ALSPAC AF: 0.747 AC: 2878

ESP6500AA AF: 0.767 AC: 3375

ESP6500EA AF: 0.740 AC: 6360

ExAC AF: 0.726 AC: 88115

Asia WGS AF: 0.753 AC: 2620 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)
-	-	1	FABP2 POLYMORPHISM (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.070
BayesDel_addAF	Benign	-0.84	T
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.39
DANN	Benign	0.78
Eigen	Benign	-0.65
Eigen_PC	Benign	-0.79
FATHMM_MKL	Benign	0.24	N
MetaRNN	Benign	0.0000015	T
MetaSVM	Benign	-1.1	T
PhyloP100		0.41
PrimateAI	Benign	0.24	T
PROVEAN	Uncertain	-3.8	D
REVEL	Benign	0.072
Sift	Benign	0.032	D
Sift4G	Benign	0.22	T
Vest4		0.027
MPC		0.10
ClinPred		0.020	T
GERP RS		0.048
gMVP		0.55
Mutation Taster		=98/2	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

Other links and lift over

dbSNP: rs1799883; hg19: chr4-120241902; COSMIC: COSV56788103;