4-119322356-T-C

Variant names:

• chr4-119322356-T-C
• rs6857641
• ENST00000720595.1:n.176-11972T>C

Variant summary

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

The ENST00000720595.1(ENSG00000294020):​n.176-11972T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 386,000 control chromosomes in the GnomAD database, including 62,260 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.57 (24456 hom., cov: 32)
  • Exomes 𝑓: 0.57 (37804 hom.)
• Consequence: ENSG00000294020 ENST00000720595.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.598
• Publications: 10 publications found

Genes affected

ENSG00000294020 (HGNC:):

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 4-119322356-T-C is Benign according to our data. Variant chr4-119322356-T-C is described in ClinVar as Benign. ClinVar VariationId is 1268685.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720595.1. 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.-254A>G		upstream_gene	N/A	NP_000125.2	P12104

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294020	ENST00000720595.1		n.176-11972T>C		intron	N/A
	ENSG00000294020	ENST00000720596.1		n.224-11972T>C		intron	N/A
	ENSG00000294020	ENST00000720597.1		n.238-11972T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86053 AN: 151814 Hom.: 24423 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.596

GnomAD4 exome AF: 0.566 AC: 132408 AN: 234068 Hom.: 37804 Cov.: 0 AF XY: 0.565 AC XY: 67952 AN XY: 120234

African (AFR) AF: 0.561 AC: 3765 AN: 6708

American (AMR) AF: 0.630 AC: 5252 AN: 8342

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 5417 AN: 8526

East Asian (EAS) AF: 0.549 AC: 11113 AN: 20238

South Asian (SAS) AF: 0.524 AC: 3202 AN: 6112

European-Finnish (FIN) AF: 0.512 AC: 9163 AN: 17888

Middle Eastern (MID) AF: 0.547 AC: 646 AN: 1180

European-Non Finnish (NFE) AF: 0.567 AC: 84904 AN: 149868

Other (OTH) AF: 0.588 AC: 8946 AN: 15206

GnomAD4 genome AF: 0.567 AC: 86151 AN: 151932 Hom.: 24456 Cov.: 32 AF XY: 0.564 AC XY: 41868 AN XY: 74244

African (AFR) AF: 0.559 AC: 23154 AN: 41430

American (AMR) AF: 0.605 AC: 9220 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2155 AN: 3468

East Asian (EAS) AF: 0.628 AC: 3248 AN: 5168

South Asian (SAS) AF: 0.533 AC: 2569 AN: 4818

European-Finnish (FIN) AF: 0.512 AC: 5400 AN: 10552

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.568 AC: 38559 AN: 67938

Other (OTH) AF: 0.599 AC: 1267 AN: 2114

Alfa AF: 0.570 Hom.: 5688

Bravo AF: 0.579

Asia WGS AF: 0.634 AC: 2206 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.33
PhyloP100		-0.60
PromoterAI		0.0087	Neutral
Mutation Taster		=300/0	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: rs6857641; hg19: chr4-120243511; COSMIC: COSV56789133;