chr2-88123239-G-A

Position:

• chr2-88123239-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001443.3(FABP1):​c.334-135C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 709,064 control chromosomes in the GnomAD database, including 19,880 homozygotes. 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: 𝑓 0.17 (3041 hom., cov: 33)
  • Exomes 𝑓: 0.22 (16839 hom.)
• Consequence: FABP1 NM_001443.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

Genes affected

FABP1 (HGNC:3555): (fatty acid binding protein 1) This gene encodes the fatty acid binding protein found in liver. Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. This protein and FABP6 (the ileal fatty acid binding protein) are also able to bind bile acids. It is thought that FABPs roles include fatty acid uptake, transport, and metabolism. [provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FABP1	NM_001443.3	c.334-135C>T		intron_variant		ENST00000295834.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP1	ENST00000295834.8	c.334-135C>T		intron_variant		1	NM_001443.3	P1
FABP1	ENST00000393750.3	c.*1213C>T		3_prime_UTR_variant	3/3	2
FABP1	ENST00000495375.1	n.1874C>T		non_coding_transcript_exon_variant	4/4	3

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26588 AN: 152048 Hom.: 3036 Cov.: 33

Gnomad AFR AF: 0.0981

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.170

GnomAD4 exome AF: 0.218 AC: 121682 AN: 556898 Hom.: 16839 Cov.: 7 AF XY: 0.228 AC XY: 66600 AN XY: 292082

Gnomad4 AFR exome AF: 0.0869

Gnomad4 AMR exome AF: 0.124

Gnomad4 ASJ exome AF: 0.157

Gnomad4 EAS exome AF: 0.508

Gnomad4 SAS exome AF: 0.443

Gnomad4 FIN exome AF: 0.122

Gnomad4 NFE exome AF: 0.191

Gnomad4 OTH exome AF: 0.206

GnomAD4 genome AF: 0.175 AC: 26594 AN: 152166 Hom.: 3041 Cov.: 33 AF XY: 0.179 AC XY: 13320 AN XY: 74390

Gnomad4 AFR AF: 0.0978

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.177

Alfa AF: 0.204 Hom.: 1663

Bravo AF: 0.166

Asia WGS AF: 0.453 AC: 1572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.44

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: rs2197076; hg19: chr2-88422758; COSMIC: COSV55558567; COSMIC: COSV55558567;