chr1-112918054-CAATAAATAAATAAATAAATAAATAAATAAATA-C

Variant names:

• chr1-112918054-CAATAAATAAATAAATAAATAAATAAATAAATA-C
• NM_003051.4:c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT

Variant summary

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

The NM_003051.4(SLC16A1):​c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT variant causes a intron change. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC16A1 NM_003051.4 intron
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• 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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A1	NM_003051.4	c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT		intron_variant	Intron 3 of 4	ENST00000369626.8	NP_003042.3
SLC16A1	NM_001166496.2	c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT		intron_variant	Intron 3 of 4		NP_001159968.1
SLC16A1	XM_047428789.1	c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT		intron_variant	Intron 3 of 4		XP_047284745.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A1	ENST00000369626.8	c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT		intron_variant	Intron 3 of 4	1	NM_003051.4	ENSP00000358640.4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 715204 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 362048

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Dec 07, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 3 of the SLC16A1 gene. It does not directly change the encoded amino acid sequence of the SLC16A1 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SLC16A1-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the effect of this variant on mRNA splicing is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

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: chr1-113460676;