chr4-119320519-C-T

Variant names:

• chr4-119320519-C-T
• rs10003567
• NM_000134.4:c.240+151G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000134.4(FABP2):​c.240+151G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 562,374 control chromosomes in the GnomAD database, including 28,635 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.34 (8816 hom., cov: 32)
  • Exomes 𝑓: 0.30 (19819 hom.)
• Consequence: FABP2 NM_000134.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.51
• Publications: 4 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 4-119320519-C-T is Benign according to our data. Variant chr4-119320519-C-T is described in ClinVar as Benign. ClinVar VariationId is 1289789.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000134.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP2	NM_000134.4	MANE Select	c.240+151G>A		intron	N/A	NP_000125.2	P12104

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP2	ENST00000274024.4	TSL:1 MANE Select	c.240+151G>A		intron	N/A	ENSP00000274024.3	P12104
	ENSG00000294020	ENST00000720595.1		n.176-13809C>T		intron	N/A
	ENSG00000294020	ENST00000720596.1		n.224-13809C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51166 AN: 151588 Hom.: 8800 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.343

GnomAD4 exome AF: 0.304 AC: 124979 AN: 410670 Hom.: 19819 AF XY: 0.298 AC XY: 64541 AN XY: 216706

African (AFR) AF: 0.375 AC: 3268 AN: 8704

American (AMR) AF: 0.312 AC: 2936 AN: 9414

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 2680 AN: 12578

East Asian (EAS) AF: 0.337 AC: 8265 AN: 24552

South Asian (SAS) AF: 0.197 AC: 6434 AN: 32736

European-Finnish (FIN) AF: 0.289 AC: 8362 AN: 28956

Middle Eastern (MID) AF: 0.277 AC: 524 AN: 1890

European-Non Finnish (NFE) AF: 0.317 AC: 85052 AN: 267956

Other (OTH) AF: 0.312 AC: 7458 AN: 23884

GnomAD4 genome AF: 0.338 AC: 51226 AN: 151704 Hom.: 8816 Cov.: 32 AF XY: 0.335 AC XY: 24824 AN XY: 74114

African (AFR) AF: 0.386 AC: 15964 AN: 41388

American (AMR) AF: 0.309 AC: 4706 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3466

East Asian (EAS) AF: 0.388 AC: 1998 AN: 5150

South Asian (SAS) AF: 0.209 AC: 1009 AN: 4822

European-Finnish (FIN) AF: 0.297 AC: 3131 AN: 10526

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22579 AN: 67814

Other (OTH) AF: 0.344 AC: 724 AN: 2102

Alfa AF: 0.327 Hom.: 1117

Bravo AF: 0.348

Asia WGS AF: 0.294 AC: 1021 AN: 3476

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.33
PhyloP100		-1.5
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: rs10003567; hg19: chr4-120241674; COSMIC: COSV56789115;