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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003051.4. 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.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT		intron	N/A	NP_003042.3
	SLC16A1	NM_001166496.2		c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT		intron	N/A	NP_001159968.1	P53985-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC16A1	ENST00000369626.8	TSL:1 MANE Select	c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT	intron	N/A	ENSP00000358640.4	P53985-1
SLC16A1	ENST00000429288.2	TSL:3	c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT	intron	N/A	ENSP00000397106.2	P53985-1
SLC16A1	ENST00000443580.6	TSL:3	c.362-42_362-11delTATTTATTTATTTATTTATTTATTTATTTATT	intron	N/A	ENSP00000399104.2	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

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over