4-119319647-CATAATAATAATAATA-CATAATA

Variant names:

• chr4-119319647-CATAATAATA-C
• rs71595363
• NM_000134.4:c.241-13_241-5delTATTATTAT

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_000134.4(FABP2):​c.241-13_241-5delTATTATTAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000291 in 798,106 control chromosomes in the GnomAD database, including 14 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00011 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00033 (14 hom.)
• Consequence: FABP2 NM_000134.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 3 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 14 AR gene

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.241-13_241-5delTATTATTAT		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.241-13_241-5delTATTATTAT		splice_region intron	N/A	ENSP00000274024.3	P12104
	ENSG00000294020	ENST00000720595.1		n.176-14680_176-14672delATAATAATA		intron	N/A
	ENSG00000294020	ENST00000720596.1		n.224-14680_224-14672delATAATAATA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000110 AC: 16 AN: 144912 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00131

Gnomad FIN AF: 0.000232

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000121

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000331 AC: 216 AN: 653182 Hom.: 14 AF XY: 0.000364 AC XY: 123 AN XY: 338314

African (AFR) AF: 0.000158 AC: 2 AN: 12696

American (AMR) AF: 0.00 AC: 0 AN: 14590

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

East Asian (EAS) AF: 0.000134 AC: 3 AN: 22330

South Asian (SAS) AF: 0.00213 AC: 78 AN: 36674

European-Finnish (FIN) AF: 0.000670 AC: 19 AN: 28340

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

European-Non Finnish (NFE) AF: 0.000202 AC: 99 AN: 491156

Other (OTH) AF: 0.000513 AC: 15 AN: 29234

GnomAD4 genome AF: 0.000110 AC: 16 AN: 144924 Hom.: 0 Cov.: 0 AF XY: 0.000114 AC XY: 8 AN XY: 70302

African (AFR) AF: 0.00 AC: 0 AN: 39692

American (AMR) AF: 0.00 AC: 0 AN: 14318

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3414

East Asian (EAS) AF: 0.00 AC: 0 AN: 4960

South Asian (SAS) AF: 0.00132 AC: 6 AN: 4556

European-Finnish (FIN) AF: 0.000232 AC: 2 AN: 8618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 278

European-Non Finnish (NFE) AF: 0.000121 AC: 8 AN: 66228

Other (OTH) AF: 0.00 AC: 0 AN: 1972

Alfa AF: 0.00 Hom.: 121

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;