chr6-122780453-GA-G

Variant names:

• chr6-122780453-GA-G
• rs431905492
• NM_001446.5:c.239delA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001446.5(FABP7):​c.239delA​(p.Asn80ThrfsTer27) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as not provided (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: FABP7 NM_001446.5 frameshift
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 0.193
• Publications: 2 publications found

Genes affected

FABP7 (HGNC:3562): (fatty acid binding protein 7) The gene encodes a small, highly conserved cytoplasmic protein that bind long-chain fatty acids and other hydrophobic ligands. The encoded protein is important in the establishment of the radial glial fiber in the developing brain. Alternative splicing and promoter usage results in multiple transcript variants encoding different isoforms. Pseudogenes of this gene are found on multiple chromosomes. [provided by RefSeq, Jan 2016]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001446.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP7	NM_001446.5	MANE Select	c.239delA	p.Asn80ThrfsTer27	frameshift	Exon 2 of 4	NP_001437.1
	FABP7	NM_001319039.2		c.239delA	p.Asn80ThrfsTer27	frameshift	Exon 2 of 3	NP_001305968.1
	FABP7	NM_001319042.2		c.227delA	p.Asn76ThrfsTer27	frameshift	Exon 2 of 4	NP_001305971.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP7	ENST00000368444.8	TSL:1 MANE Select	c.239delA	p.Asn80ThrfsTer27	frameshift	Exon 2 of 4	ENSP00000357429.3
	FABP7	ENST00000356535.4	TSL:1	c.239delA	p.Asn80ThrfsTer27	frameshift	Exon 2 of 3	ENSP00000348931.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

Laboratory for Molecular Psychiatry, RIKEN

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.19
Mutation Taster		=5/195	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs431905492; hg19: chr6-123101598;