1-112918054-CAATAAATAAATAAATAAATAAATA-CAATAAATA

Position:

• chr1-112918054-CAATAAATAAATAAATAAATAAATA-CAATAAATA

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_003051.4(SLC16A1):​c.362-26_362-11del variant causes a splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.0139 in 859,730 control chromosomes in the GnomAD database, including 831 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.014 (32 hom., cov: 0)
  • Exomes 𝑓: 0.014 (799 hom.)
• Consequence: SLC16A1 NM_003051.4 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 3.97

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]

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP6: Variant 1-112918054-CAATAAATAAATAAATA-C is Benign according to our data. Variant chr1-112918054-CAATAAATAAATAAATA-C is described in ClinVar as [Likely_benign]. Clinvar id is 1570647.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A1	NM_003051.4	c.362-26_362-11del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000369626.8	NP_003042.3
SLC16A1	NM_001166496.2	c.362-26_362-11del		splice_polypyrimidine_tract_variant, intron_variant			NP_001159968.1
SLC16A1	XM_047428789.1	c.362-26_362-11del		splice_polypyrimidine_tract_variant, intron_variant			XP_047284745.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A1	ENST00000369626.8	c.362-26_362-11del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_003051.4	ENSP00000358640	P1

Frequencies

GnomAD3 genomes AF: 0.0136 AC: 1963 AN: 144554 Hom.: 30 Cov.: 0

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0145

Gnomad ASJ AF: 0.00116

Gnomad EAS AF: 0.0581

Gnomad SAS AF: 0.0324

Gnomad FIN AF: 0.00614

Gnomad MID AF: 0.00325

Gnomad NFE AF: 0.00888

Gnomad OTH AF: 0.0106

GnomAD3 exomes AF: 0.0162 AC: 985 AN: 60732 Hom.: 202 AF XY: 0.0172 AC XY: 612 AN XY: 35678

Gnomad AFR exome AF: 0.00483

Gnomad AMR exome AF: 0.0193

Gnomad ASJ exome AF: 0.00462

Gnomad EAS exome AF: 0.130

Gnomad SAS exome AF: 0.0424

Gnomad FIN exome AF: 0.00424

Gnomad NFE exome AF: 0.00447

Gnomad OTH exome AF: 0.00874

GnomAD4 exome AF: 0.0139 AC: 9965 AN: 715104 Hom.: 799 AF XY: 0.0148 AC XY: 5341 AN XY: 361992

Gnomad4 AFR exome AF: 0.0204

Gnomad4 AMR exome AF: 0.0235

Gnomad4 ASJ exome AF: 0.00322

Gnomad4 EAS exome AF: 0.0824

Gnomad4 SAS exome AF: 0.0715

Gnomad4 FIN exome AF: 0.00854

Gnomad4 NFE exome AF: 0.00881

Gnomad4 OTH exome AF: 0.0142

GnomAD4 genome AF: 0.0136 AC: 1966 AN: 144626 Hom.: 32 Cov.: 0 AF XY: 0.0147 AC XY: 1034 AN XY: 70212

Gnomad4 AFR AF: 0.0167

Gnomad4 AMR AF: 0.0149

Gnomad4 ASJ AF: 0.00116

Gnomad4 EAS AF: 0.0584

Gnomad4 SAS AF: 0.0319

Gnomad4 FIN AF: 0.00614

Gnomad4 NFE AF: 0.00888

Gnomad4 OTH AF: 0.0100

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Metabolic myopathy due to lactate transporter defect;C1864902:Exercise-induced hyperinsulinism;C4015186:Ketoacidosis due to monocarboxylate transporter-1 deficiency Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Jan 21, 2022

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

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: rs149491709; hg19: chr1-113460676;