rs606231172

Variant names:

• chr1-112956380-C-CCCCCACCCCGCCACGTGACCGGCGT
• rs606231172
• ENST00000429288.2:c.-45+458_-45+459insACGCCGGTCACGTGGCGGGGTGGGG

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]

SLC16A1-AS1 (HGNC:49445): (SLC16A1 antisense RNA 1)

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 rank	MANE	Protein	UniProt
SLC16A1	NM_003051.4	c.-391_-390insACGCCGGTCACGTGGCGGGGTGGGG		upstream_gene_variant		ENST00000369626.8	NP_003042.3
SLC16A1	NM_001166496.2	c.-1150_-1149insACGCCGGTCACGTGGCGGGGTGGGG		upstream_gene_variant			NP_001159968.1
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 rank	TSL	MANE	Protein	Appris	UniProt
SLC16A1	ENST00000369626.8	c.-391_-390insACGCCGGTCACGTGGCGGGGTGGGG		upstream_gene_variant		1	NM_003051.4	ENSP00000358640.4

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

Sep 01, 2007

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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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;