dbSNP rs149491709: SLC16A1:c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT (chr1-112918054-CAATAAATAAATAAATAAATAAATAAATAAATA-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_003051.4(SLC16A1):c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT variant causes a intron change. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.97

Publications

0 publications found

Variant links:

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 links:

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

SLC16A1-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SLC16A1	NM_003051.4 link	c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT	intron_variant	Intron 3 of 4	ENST00000369626.8	NP_003042.3	P53985-1A0A024R0H1
SLC16A1	NM_001166496.2 link	c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT	intron_variant	Intron 3 of 4		NP_001159968.1	P53985-1A0A024R0H1B4DKS0
SLC16A1	XM_047428789.1 link	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 link	c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT		intron_variant	Intron 3 of 4	1	NM_003051.4	ENSP00000358640.4		P53985-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

715204

Hom.:

AF XY:

0.00

AC XY:

AN XY:

362048

African (AFR)

AF:

0.00

AC:

AN:

14652

American (AMR)

AF:

0.00

AC:

AN:

12942

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14304

East Asian (EAS)

AF:

0.00

AC:

AN:

24300

South Asian (SAS)

AF:

0.00

AC:

AN:

22964

European-Finnish (FIN)

AF:

0.00

AC:

AN:

20956

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2214

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

572114

Other (OTH)

AF:

0.00

AC:

AN:

30758

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

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

Name

Calibrated prediction

Score

Prediction

PhyloP100

4.0

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over