rs606231172

Variant names:

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

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. 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. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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
• Publications: 1 publications found

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

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PP5: Variant 1-112956380-C-CCCCCACCCCGCCACGTGACCGGCGT is Pathogenic according to our data. Variant chr1-112956380-C-CCCCCACCCCGCCACGTGACCGGCGT is described in ClinVar as Pathogenic. ClinVar VariationId is 8917.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429288.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A1	NM_003051.4	MANE Select	c.-391_-390insACGCCGGTCACGTGGCGGGGTGGGG		upstream_gene	N/A	NP_003042.3
	SLC16A1	NM_001166496.2		c.-1150_-1149insACGCCGGTCACGTGGCGGGGTGGGG		upstream_gene	N/A	NP_001159968.1	P53985-1
	SLC16A1-AS1	NR_103743.1		n.-35_-34insCCCCACCCCGCCACGTGACCGGCGT		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A1	ENST00000429288.2	TSL:3	c.-45+458_-45+459insACGCCGGTCACGTGGCGGGGTGGGG		intron	N/A	ENSP00000397106.2	P53985-1
	SLC16A1	ENST00000679803.1		c.-45+1157_-45+1158insACGCCGGTCACGTGGCGGGGTGGGG		intron	N/A	ENSP00000505879.1	P53985-1
	SLC16A1	ENST00000913229.1		c.-45+727_-45+728insACGCCGGTCACGTGGCGGGGTGGGG		intron	N/A	ENSP00000583288.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
1	-	-	Exercise-induced hyperinsulinism (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs606231172; hg19: chr1-113499002;