4-119319647-C-CATAATAATAATA

Position:

• chr4-119319647-C-CATAATAATAATA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP6_Very_Strong

The NM_000134.4(FABP2):​c.241-16_241-5dupTATTATTATTAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.070 (491 hom., cov: 0)
  • Exomes 𝑓: 0.021 (228 hom.)
  • Failed GnomAD Quality Control
• Consequence: FABP2 NM_000134.4 splice_region, intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• 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 -8 ACMG points.

• BP6: Variant 4-119319647-C-CATAATAATAATA is Benign according to our data. Variant chr4-119319647-C-CATAATAATAATA is described in ClinVar as [Benign]. Clinvar id is 767974.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FABP2	NM_000134.4	c.241-16_241-5dupTATTATTATTAT		splice_region_variant, intron_variant		ENST00000274024.4	NP_000125.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FABP2	ENST00000274024.4	c.241-16_241-5dupTATTATTATTAT		splice_region_variant, intron_variant		1	NM_000134.4	ENSP00000274024.3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 10128 AN: 144760 Hom.: 488 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.0284

Gnomad EAS AF: 0.0376

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0467

Gnomad MID AF: 0.0296

Gnomad NFE AF: 0.0430

Gnomad OTH AF: 0.0705

GnomAD3 exomes AF: 0.0204 AC: 1530 AN: 75038 Hom.: 34 AF XY: 0.0200 AC XY: 868 AN XY: 43318

Gnomad AFR exome AF: 0.0212

Gnomad AMR exome AF: 0.0119

Gnomad ASJ exome AF: 0.0237

Gnomad EAS exome AF: 0.0125

Gnomad SAS exome AF: 0.0129

Gnomad FIN exome AF: 0.0251

Gnomad NFE exome AF: 0.0227

Gnomad OTH exome AF: 0.0248

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0211 AC: 13722 AN: 650314 Hom.: 228 Cov.: 12 AF XY: 0.0216 AC XY: 7285 AN XY: 336682

Gnomad4 AFR exome AF: 0.0741

Gnomad4 AMR exome AF: 0.0217

Gnomad4 ASJ exome AF: 0.0176

Gnomad4 EAS exome AF: 0.0173

Gnomad4 SAS exome AF: 0.00735

Gnomad4 FIN exome AF: 0.0217

Gnomad4 NFE exome AF: 0.0208

Gnomad4 OTH exome AF: 0.0259

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0701 AC: 10149 AN: 144772 Hom.: 491 Cov.: 0 AF XY: 0.0711 AC XY: 4994 AN XY: 70214

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.0581

Gnomad4 ASJ AF: 0.0284

Gnomad4 EAS AF: 0.0377

Gnomad4 SAS AF: 0.0173

Gnomad4 FIN AF: 0.0467

Gnomad4 NFE AF: 0.0430

Gnomad4 OTH AF: 0.0701

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 10, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 23, 2018	- -

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;