4-119319647-C-CATAATAATA

Position:

• chr4-119319647-C-CATAATAATA

Variant summary

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

The NM_000134.4(FABP2):​c.241-13_241-5dupTATTATTAT 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 0.22 (3714 hom., cov: 0)
  • Exomes 𝑓: 0.13 (5351 hom.)
  • Failed GnomAD Quality Control
• Consequence: FABP2 NM_000134.4 splice_region, 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-CATAATAATA is Benign according to our data. Variant chr4-119319647-C-CATAATAATA is described in ClinVar as [Benign]. Clinvar id is 1265548.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FABP2	NM_000134.4	c.241-13_241-5dupTATTATTAT		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.241-13_241-5dupTATTATTAT		splice_region_variant, intron_variant		1	NM_000134.4	ENSP00000274024.3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 31339 AN: 144680 Hom.: 3715 Cov.: 0

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.216

GnomAD3 exomes AF: 0.110 AC: 8240 AN: 75038 Hom.: 558 AF XY: 0.112 AC XY: 4851 AN XY: 43318

Gnomad AFR exome AF: 0.0258

Gnomad AMR exome AF: 0.0474

Gnomad ASJ exome AF: 0.103

Gnomad EAS exome AF: 0.0591

Gnomad SAS exome AF: 0.124

Gnomad FIN exome AF: 0.144

Gnomad NFE exome AF: 0.120

Gnomad OTH exome AF: 0.0986

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.125 AC: 81345 AN: 648982 Hom.: 5351 Cov.: 12 AF XY: 0.129 AC XY: 43232 AN XY: 336088

Gnomad4 AFR exome AF: 0.0775

Gnomad4 AMR exome AF: 0.107

Gnomad4 ASJ exome AF: 0.0858

Gnomad4 EAS exome AF: 0.180

Gnomad4 SAS exome AF: 0.0750

Gnomad4 FIN exome AF: 0.116

Gnomad4 NFE exome AF: 0.130

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.216 AC: 31324 AN: 144688 Hom.: 3714 Cov.: 0 AF XY: 0.213 AC XY: 14941 AN XY: 70174

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.217

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

- -

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;