4-119319026-C-T

Variant names:

• chr4-119319026-C-T
• rs1511024
• NM_000134.4:c.*15G>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000134.4(FABP2):​c.*15G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 1,585,764 control chromosomes in the GnomAD database, including 1,113 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.041 (193 hom., cov: 32)
  • Exomes 𝑓: 0.033 (920 hom.)
• Consequence: FABP2 NM_000134.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.286
• Publications: 9 publications found

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]

ENSG00000294020 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 4-119319026-C-T is Benign according to our data. Variant chr4-119319026-C-T is described in ClinVar as Benign. ClinVar VariationId is 1226479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP2	NM_000134.4	c.*15G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000274024.4	NP_000125.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP2	ENST00000274024.4	c.*15G>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_000134.4	ENSP00000274024.3

Frequencies

GnomAD3 genomes AF: 0.0414 AC: 6292 AN: 151858 Hom.: 191 Cov.: 32

Gnomad AFR AF: 0.0642

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.00578

Gnomad SAS AF: 0.0321

Gnomad FIN AF: 0.0373

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0418

GnomAD2 exomes AF: 0.0325 AC: 7602 AN: 234116 AF XY: 0.0330

Gnomad AFR exome AF: 0.0629

Gnomad AMR exome AF: 0.0185

Gnomad ASJ exome AF: 0.0164

Gnomad EAS exome AF: 0.00569

Gnomad FIN exome AF: 0.0377

Gnomad NFE exome AF: 0.0352

Gnomad OTH exome AF: 0.0385

GnomAD4 exome AF: 0.0329 AC: 47174 AN: 1433788 Hom.: 920 Cov.: 28 AF XY: 0.0330 AC XY: 23580 AN XY: 714010

African (AFR) AF: 0.0584 AC: 1849 AN: 31654

American (AMR) AF: 0.0212 AC: 864 AN: 40736

Ashkenazi Jewish (ASJ) AF: 0.0168 AC: 432 AN: 25770

East Asian (EAS) AF: 0.0147 AC: 557 AN: 37788

South Asian (SAS) AF: 0.0372 AC: 3099 AN: 83324

European-Finnish (FIN) AF: 0.0388 AC: 2062 AN: 53128

Middle Eastern (MID) AF: 0.104 AC: 587 AN: 5658

European-Non Finnish (NFE) AF: 0.0325 AC: 35659 AN: 1096554

Other (OTH) AF: 0.0349 AC: 2065 AN: 59176

GnomAD4 genome AF: 0.0415 AC: 6301 AN: 151976 Hom.: 193 Cov.: 32 AF XY: 0.0418 AC XY: 3106 AN XY: 74292

African (AFR) AF: 0.0641 AC: 2662 AN: 41498

American (AMR) AF: 0.0339 AC: 517 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3462

East Asian (EAS) AF: 0.00580 AC: 30 AN: 5176

South Asian (SAS) AF: 0.0322 AC: 155 AN: 4818

European-Finnish (FIN) AF: 0.0373 AC: 393 AN: 10548

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0340 AC: 2309 AN: 67918

Other (OTH) AF: 0.0447 AC: 94 AN: 2104

Alfa AF: 0.0407 Hom.: 74

Bravo AF: 0.0411

Asia WGS AF: 0.0360 AC: 124 AN: 3458

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 20, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.62
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1511024; hg19: chr4-120240181;