4-119319647-C-CATA

Position:

• chr4-119319647-C-CATA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000134.4(FABP2):​c.241-5_241-4insTAT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.10 (966 hom., cov: 0)
  • Exomes 𝑓: 0.088 (1606 hom.)
• Consequence: FABP2 NM_000134.4 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.118

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 4-119319647-C-CATA is Benign according to our data. Variant chr4-119319647-C-CATA is described in ClinVar as [Benign]. Clinvar id is 1248668.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FABP2	NM_000134.4	c.241-5_241-4insTAT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000274024.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP2	ENST00000274024.4	c.241-5_241-4insTAT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_000134.4	P1

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15185 AN: 144814 Hom.: 967 Cov.: 0

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.0790

Gnomad AMR AF: 0.0879

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0789

Gnomad SAS AF: 0.0922

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.145

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.0974

GnomAD3 exomes AF: 0.0789 AC: 5921 AN: 75038 Hom.: 144 AF XY: 0.0815 AC XY: 3532 AN XY: 43318

Gnomad AFR exome AF: 0.00746

Gnomad AMR exome AF: 0.0217

Gnomad ASJ exome AF: 0.0837

Gnomad EAS exome AF: 0.0182

Gnomad SAS exome AF: 0.0974

Gnomad FIN exome AF: 0.117

Gnomad NFE exome AF: 0.0837

Gnomad OTH exome AF: 0.0782

GnomAD4 exome AF: 0.0885 AC: 57141 AN: 645770 Hom.: 1606 Cov.: 12 AF XY: 0.0908 AC XY: 30371 AN XY: 334318

Gnomad4 AFR exome AF: 0.0261

Gnomad4 AMR exome AF: 0.0402

Gnomad4 ASJ exome AF: 0.0743

Gnomad4 EAS exome AF: 0.0628

Gnomad4 SAS exome AF: 0.0614

Gnomad4 FIN exome AF: 0.101

Gnomad4 NFE exome AF: 0.0947

Gnomad4 OTH exome AF: 0.0833

GnomAD4 genome AF: 0.105 AC: 15170 AN: 144826 Hom.: 966 Cov.: 0 AF XY: 0.103 AC XY: 7227 AN XY: 70236

Gnomad4 AFR AF: 0.0360

Gnomad4 AMR AF: 0.0879

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0788

Gnomad4 SAS AF: 0.0918

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.0963

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 09, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71595363; hg19: chr4-120240802;