rs606231172

Positions:

• chr1-112956380-C-CCCCCACCCCGCCACGTGACCGGCGT

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

The ENST00000429288.2(SLC16A1):​c.-45+458_-45+459insACGCCGGTCACGTGGCGGGGTGGGG variant causes a intron 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 Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 31)
• Consequence: SLC16A1 ENST00000429288.2 intron
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: -0.732

Genes affected

SLC16A1 (HGNC:10922): (solute carrier family 16 member 1) The protein encoded by this gene is a proton-linked monocarboxylate transporter that catalyzes the movement of many monocarboxylates, such as lactate and pyruvate, across the plasma membrane. Mutations in this gene are associated with erythrocyte lactate transporter defect. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Oct 2009]

(HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-112956380-C-CCCCCACCCCGCCACGTGACCGGCGT is Pathogenic according to our data. Variant chr1-112956380-C-CCCCCACCCCGCCACGTGACCGGCGT is described in ClinVar as [Pathogenic]. Clinvar id is 8917.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.112956380_112956381insCCCCACCCCGCCACGTGACCGGCGT		intergenic_region
SLC16A1-AS1	NR_103743.1	n.-35_-34insCCCCACCCCGCCACGTGACCGGCGT		upstream_gene_variant
SLC16A1-AS1	NR_103744.1	n.-35_-34insCCCCACCCCGCCACGTGACCGGCGT		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A1	ENST00000429288.2	c.-45+458_-45+459insACGCCGGTCACGTGGCGGGGTGGGG		intron_variant		3		ENSP00000397106.2
SLC16A1	ENST00000679803.1	c.-45+1157_-45+1158insACGCCGGTCACGTGGCGGGGTGGGG		intron_variant				ENSP00000505879.1
SLC16A1-AS1	ENST00000416193.6	n.-35_-34insCCCCACCCCGCCACGTGACCGGCGT		upstream_gene_variant		1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Exercise-induced hyperinsulinism Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Sep 01, 2007

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs606231172; hg19: chr1-113499002;