chr1-112912827-C-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_003051.4(SLC16A1):​c.*1064G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00014 ( 0 hom., cov: 32)
Failed GnomAD Quality Control

Consequence

SLC16A1
NM_003051.4 3_prime_UTR

Scores

2

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.977
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC16A1NM_003051.4 linkuse as main transcriptc.*1064G>T 3_prime_UTR_variant 5/5 ENST00000369626.8 NP_003042.3
SLC16A1NM_001166496.2 linkuse as main transcriptc.*1064G>T 3_prime_UTR_variant 5/5 NP_001159968.1
SLC16A1XM_047428789.1 linkuse as main transcriptc.*1064G>T 3_prime_UTR_variant 5/5 XP_047284745.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC16A1ENST00000369626.8 linkuse as main transcriptc.*1064G>T 3_prime_UTR_variant 5/51 NM_003051.4 ENSP00000358640 P1P53985-1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
20
AN:
145574
Hom.:
0
Cov.:
32
FAILED QC
Gnomad AFR
AF:
0.000177
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000680
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000658
Gnomad FIN
AF:
0.000436
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000607
Gnomad OTH
AF:
0.000502
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000137
AC:
20
AN:
145646
Hom.:
0
Cov.:
32
AF XY:
0.000198
AC XY:
14
AN XY:
70840
show subpopulations
Gnomad4 AFR
AF:
0.000176
Gnomad4 AMR
AF:
0.0000679
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000660
Gnomad4 FIN
AF:
0.000436
Gnomad4 NFE
AF:
0.0000607
Gnomad4 OTH
AF:
0.000497
Alfa
AF:
0.00135
Hom.:
0

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Exercise-induced hyperinsulinism Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.073
DANN
Benign
0.43

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: rs886045063; hg19: chr1-113455449; API