rs1973598

Variant names:

• chr4-119322264-A-C
• rs1973598
• ENST00000720595.1:n.176-12064A>C

Your query was ambiguous. Multiple possible variants found:

• chr4-119322264-A-C
• chr4-119322264-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000720595.1(ENSG00000294020):​n.176-12064A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000294020 ENST00000720595.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 4 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP2	NM_000134.4	c.-162T>G		upstream_gene_variant		ENST00000274024.4	NP_000125.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP2	ENST00000274024.4	c.-162T>G		upstream_gene_variant		1	NM_000134.4	ENSP00000274024.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 360842 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 190052

African (AFR) AF: 0.00 AC: 0 AN: 9428

American (AMR) AF: 0.00 AC: 0 AN: 13742

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11512

East Asian (EAS) AF: 0.00 AC: 0 AN: 26786

South Asian (SAS) AF: 0.00 AC: 0 AN: 22730

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3090

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 221600

Other (OTH) AF: 0.00 AC: 0 AN: 21332

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 629

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.61
PhyloP100		-0.16
PromoterAI		-0.0093	Neutral

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: rs1973598; hg19: chr4-120243419;