GeneBe

5-128966589-G-GAGGAATCACCACACTGTCTTCCACAATGGTTGAACTAGTTTACAC

Position:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000262462.9(SLC27A6):​c.452_453insAGGAATCACCACACTGTCTTCCACAATGGTTGAACTAGTTTACAC​(p.Cys151delinsTer) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 32)

Consequence

SLC27A6
ENST00000262462.9 stop_gained

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: -1.13
Variant links:
Genes affected
SLC27A6 (HGNC:11000): (solute carrier family 27 member 6) This gene encodes a member of the fatty acid transport protein family (FATP). FATPs are involved in the uptake of long-chain fatty acids and have unique expression patterns. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC27A6NM_001017372.3 linkuse as main transcriptc.452_453insAGGAATCACCACACTGTCTTCCACAATGGTTGAACTAGTTTACAC p.Cys151delinsTer stop_gained 1/10 ENST00000262462.9 NP_001017372.1
SLC27A6NM_001317984.2 linkuse as main transcriptc.452_453insAGGAATCACCACACTGTCTTCCACAATGGTTGAACTAGTTTACAC p.Cys151delinsTer stop_gained 2/11 NP_001304913.1
SLC27A6NM_014031.5 linkuse as main transcriptc.452_453insAGGAATCACCACACTGTCTTCCACAATGGTTGAACTAGTTTACAC p.Cys151delinsTer stop_gained 2/11 NP_054750.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC27A6ENST00000262462.9 linkuse as main transcriptc.452_453insAGGAATCACCACACTGTCTTCCACAATGGTTGAACTAGTTTACAC p.Cys151delinsTer stop_gained 1/101 NM_001017372.3 ENSP00000262462 P1
SLC27A6ENST00000395266.5 linkuse as main transcriptc.452_453insAGGAATCACCACACTGTCTTCCACAATGGTTGAACTAGTTTACAC p.Cys151delinsTer stop_gained 2/111 ENSP00000378684 P1
SLC27A6ENST00000506176.1 linkuse as main transcriptc.452_453insAGGAATCACCACACTGTCTTCCACAATGGTTGAACTAGTTTACAC p.Cys151delinsTer stop_gained 2/111 ENSP00000421024 P1
SLC27A6ENST00000508645.5 linkuse as main transcriptc.-62-18544_-62-18543insAGGAATCACCACACTGTCTTCCACAATGGTTGAACTAGTTTACAC intron_variant 5 ENSP00000421759

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
34
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Hepatocellular carcinoma Pathogenic:1
Pathogenic, no assertion criteria providedresearchArun Kumar Laboratory, Indian Institute of ScienceJun 15, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-128302282; API