4-119320570-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000134.4(FABP2):c.240+100G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 909,900 control chromosomes in the GnomAD database, including 25,446 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.23 (4166 hom., cov: 32)
  • Exomes 𝑓: 0.23 (21280 hom.)
• Consequence: FABP2 NM_000134.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.06

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 4-119320570-C-A is Benign according to our data. Variant chr4-119320570-C-A is described in ClinVar as [Benign]. Clinvar id is 1263767.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FABP2	NM_000134.4	c.240+100G>T		intron_variant		ENST00000274024.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP2	ENST00000274024.4	c.240+100G>T		intron_variant		1	NM_000134.4	P1

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34745 AN: 151538 Hom.: 4159 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.254

GnomAD4 exome AF: 0.232 AC: 175594 AN: 758242 Hom.: 21280 AF XY: 0.234 AC XY: 92568 AN XY: 394790

Gnomad4 AFR exome AF: 0.168

Gnomad4 AMR exome AF: 0.308

Gnomad4 ASJ exome AF: 0.405

Gnomad4 EAS exome AF: 0.207

Gnomad4 SAS exome AF: 0.286

Gnomad4 FIN exome AF: 0.208

Gnomad4 NFE exome AF: 0.221

Gnomad4 OTH exome AF: 0.253

GnomAD4 genome AF: 0.229 AC: 34782 AN: 151658 Hom.: 4166 Cov.: 32 AF XY: 0.229 AC XY: 16990 AN XY: 74070

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.257

Alfa AF: 0.244 Hom.: 2561

Bravo AF: 0.231

Asia WGS AF: 0.338 AC: 1171 AN: 3468

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

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.42
Dann	Benign	0.43

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: rs11935130; hg19: chr4-120241725;