4-119319647-CATAATAATAATAATA-CATA

Variant names:

• chr4-119319647-CATAATAATAATA-C
• rs71595363
• NM_000134.4:c.241-16_241-5delTATTATTATTAT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000134.4(FABP2):​c.241-16_241-5delTATTATTATTAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000612 in 653,226 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000061 (0 hom.)
• Consequence: FABP2 NM_000134.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

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.241-16_241-5delTATTATTATTAT		splice_region intron	N/A	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.241-16_241-5delTATTATTATTAT		splice_region intron	N/A	ENSP00000274024.3	P12104
	ENSG00000294020	ENST00000720595.1		n.176-14680_176-14669delATAATAATAATA		intron	N/A
	ENSG00000294020	ENST00000720596.1		n.224-14680_224-14669delATAATAATAATA		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000612 AC: 4 AN: 653226 Hom.: 0 AF XY: 0.00000591 AC XY: 2 AN XY: 338340

African (AFR) AF: 0.00 AC: 0 AN: 12708

American (AMR) AF: 0.00 AC: 0 AN: 14592

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15978

East Asian (EAS) AF: 0.00 AC: 0 AN: 22330

South Asian (SAS) AF: 0.0000545 AC: 2 AN: 36672

European-Finnish (FIN) AF: 0.0000353 AC: 1 AN: 28340

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2184

European-Non Finnish (NFE) AF: 0.00000204 AC: 1 AN: 491176

Other (OTH) AF: 0.00 AC: 0 AN: 29246

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs71595363; hg19: chr4-120240802;