4-119319647-CATA-C

Position:

• chr4-119319647-CATA-C

Variant summary

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

The NM_000134.4(FABP2):​c.241-7_241-5delTAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 787,412 control chromosomes in the GnomAD database, including 1,250 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.067 (971 hom., cov: 0)
  • Exomes 𝑓: 0.014 (279 hom.)
• Consequence: FABP2 NM_000134.4 splice_region, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.189

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-CATA-C is Benign according to our data. Variant chr4-119319647-CATA-C is described in ClinVar as [Benign]. Clinvar id is 1250553.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FABP2	NM_000134.4	c.241-7_241-5delTAT		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.241-7_241-5delTAT		splice_region_variant, intron_variant		1	NM_000134.4	ENSP00000274024.3

Frequencies

GnomAD3 genomes AF: 0.0669 AC: 9689 AN: 144844 Hom.: 969 Cov.: 0

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0296

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0579

Gnomad SAS AF: 0.0212

Gnomad FIN AF: 0.000581

Gnomad MID AF: 0.0132

Gnomad NFE AF: 0.00181

Gnomad OTH AF: 0.0541

GnomAD3 exomes AF: 0.0108 AC: 808 AN: 75038 Hom.: 47 AF XY: 0.0102 AC XY: 440 AN XY: 43318

Gnomad AFR exome AF: 0.0924

Gnomad AMR exome AF: 0.0105

Gnomad ASJ exome AF: 0.00431

Gnomad EAS exome AF: 0.0246

Gnomad SAS exome AF: 0.0161

Gnomad FIN exome AF: 0.00406

Gnomad NFE exome AF: 0.00307

Gnomad OTH exome AF: 0.00868

GnomAD4 exome AF: 0.0142 AC: 9141 AN: 642556 Hom.: 279 AF XY: 0.0136 AC XY: 4533 AN XY: 332516

Gnomad4 AFR exome AF: 0.210

Gnomad4 AMR exome AF: 0.0201

Gnomad4 ASJ exome AF: 0.00800

Gnomad4 EAS exome AF: 0.0695

Gnomad4 SAS exome AF: 0.0184

Gnomad4 FIN exome AF: 0.00708

Gnomad4 NFE exome AF: 0.00594

Gnomad4 OTH exome AF: 0.0275

GnomAD4 genome AF: 0.0670 AC: 9708 AN: 144856 Hom.: 971 Cov.: 0 AF XY: 0.0655 AC XY: 4600 AN XY: 70266

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.0296

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0581

Gnomad4 SAS AF: 0.0206

Gnomad4 FIN AF: 0.000581

Gnomad4 NFE AF: 0.00181

Gnomad4 OTH AF: 0.0538

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

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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;