chr1-112918054-CAATA-C
Position:
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The ENST00000369626.8(SLC16A1):c.362-14_362-11del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 855,896 control chromosomes in the GnomAD database, including 143,238 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.62 ( 27489 hom., cov: 0)
Exomes 𝑓: 0.52 ( 115749 hom. )
Consequence
SLC16A1
ENST00000369626.8 splice_polypyrimidine_tract, intron
ENST00000369626.8 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.375
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 1-112918054-CAATA-C is Benign according to our data. Variant chr1-112918054-CAATA-C is described in ClinVar as [Likely_benign]. Clinvar id is 291868.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-112918054-CAATA-C is described in Lovd as [Likely_benign].
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC16A1 | NM_003051.4 | c.362-14_362-11del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000369626.8 | NP_003042.3 | |||
SLC16A1 | NM_001166496.2 | c.362-14_362-11del | splice_polypyrimidine_tract_variant, intron_variant | NP_001159968.1 | ||||
SLC16A1 | XM_047428789.1 | c.362-14_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.362-14_362-11del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003051.4 | ENSP00000358640 | P1 |
Frequencies
GnomAD3 genomes AF: 0.616 AC: 88865AN: 144204Hom.: 27482 Cov.: 0
GnomAD3 genomes
AF:
AC:
88865
AN:
144204
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.322 AC: 19552AN: 60732Hom.: 6587 AF XY: 0.332 AC XY: 11832AN XY: 35678
GnomAD3 exomes
AF:
AC:
19552
AN:
60732
Hom.:
AF XY:
AC XY:
11832
AN XY:
35678
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.517 AC: 368245AN: 711622Hom.: 115749 AF XY: 0.520 AC XY: 187468AN XY: 360180
GnomAD4 exome
AF:
AC:
368245
AN:
711622
Hom.:
AF XY:
AC XY:
187468
AN XY:
360180
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.616 AC: 88894AN: 144274Hom.: 27489 Cov.: 0 AF XY: 0.616 AC XY: 43142AN XY: 70026
GnomAD4 genome
AF:
AC:
88894
AN:
144274
Hom.:
Cov.:
0
AF XY:
AC XY:
43142
AN XY:
70026
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Hyperinsulinism, Dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
SLC16A1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 18, 2021 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at