chr1-112918054-CAATA-C

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

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.375
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]

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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
SLC16A1NM_003051.4 linkuse as main transcriptc.362-14_362-11del splice_polypyrimidine_tract_variant, intron_variant ENST00000369626.8 NP_003042.3
SLC16A1NM_001166496.2 linkuse as main transcriptc.362-14_362-11del splice_polypyrimidine_tract_variant, intron_variant NP_001159968.1
SLC16A1XM_047428789.1 linkuse as main transcriptc.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
SLC16A1ENST00000369626.8 linkuse as main transcriptc.362-14_362-11del splice_polypyrimidine_tract_variant, intron_variant 1 NM_003051.4 ENSP00000358640 P1P53985-1

Frequencies

GnomAD3 genomes
AF:
0.616
AC:
88865
AN:
144204
Hom.:
27482
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.587
Gnomad AMI
AF:
0.777
Gnomad AMR
AF:
0.629
Gnomad ASJ
AF:
0.713
Gnomad EAS
AF:
0.640
Gnomad SAS
AF:
0.724
Gnomad FIN
AF:
0.553
Gnomad MID
AF:
0.682
Gnomad NFE
AF:
0.622
Gnomad OTH
AF:
0.600
GnomAD3 exomes
AF:
0.322
AC:
19552
AN:
60732
Hom.:
6587
AF XY:
0.332
AC XY:
11832
AN XY:
35678
show subpopulations
Gnomad AFR exome
AF:
0.0679
Gnomad AMR exome
AF:
0.241
Gnomad ASJ exome
AF:
0.613
Gnomad EAS exome
AF:
0.318
Gnomad SAS exome
AF:
0.515
Gnomad FIN exome
AF:
0.347
Gnomad NFE exome
AF:
0.275
Gnomad OTH exome
AF:
0.362
GnomAD4 exome
AF:
0.517
AC:
368245
AN:
711622
Hom.:
115749
AF XY:
0.520
AC XY:
187468
AN XY:
360180
show subpopulations
Gnomad4 AFR exome
AF:
0.449
Gnomad4 AMR exome
AF:
0.452
Gnomad4 ASJ exome
AF:
0.654
Gnomad4 EAS exome
AF:
0.627
Gnomad4 SAS exome
AF:
0.544
Gnomad4 FIN exome
AF:
0.488
Gnomad4 NFE exome
AF:
0.511
Gnomad4 OTH exome
AF:
0.548
GnomAD4 genome
AF:
0.616
AC:
88894
AN:
144274
Hom.:
27489
Cov.:
0
AF XY:
0.616
AC XY:
43142
AN XY:
70026
show subpopulations
Gnomad4 AFR
AF:
0.587
Gnomad4 AMR
AF:
0.629
Gnomad4 ASJ
AF:
0.713
Gnomad4 EAS
AF:
0.640
Gnomad4 SAS
AF:
0.724
Gnomad4 FIN
AF:
0.553
Gnomad4 NFE
AF:
0.622
Gnomad4 OTH
AF:
0.603

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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024- -
Benign, criteria provided, single submitterclinical testingGeneDxJun 09, 2021- -
Hyperinsulinism, Dominant Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
SLC16A1-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesJun 18, 2021This 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs149491709; hg19: chr1-113460676; API