1-112912805-TA-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2

The NM_003051.4(SLC16A1):​c.*1085del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00766 in 136,438 control chromosomes in the GnomAD database, including 9 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0077 ( 9 hom., cov: 32)
Failed GnomAD Quality Control

Consequence

SLC16A1
NM_003051.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.312
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 -5 ACMG points.

BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00766 (1045/136438) while in subpopulation AFR AF= 0.0232 (865/37318). AF 95% confidence interval is 0.0219. There are 9 homozygotes in gnomad4. There are 497 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High Homozygotes in GnomAd4 at 9 SD gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC16A1NM_003051.4 linkuse as main transcriptc.*1085del 3_prime_UTR_variant 5/5 ENST00000369626.8 NP_003042.3
SLC16A1NM_001166496.2 linkuse as main transcriptc.*1085del 3_prime_UTR_variant 5/5 NP_001159968.1
SLC16A1XM_047428789.1 linkuse as main transcriptc.*1085del 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.*1085del 3_prime_UTR_variant 5/51 NM_003051.4 ENSP00000358640 P1P53985-1

Frequencies

GnomAD3 genomes
AF:
0.00760
AC:
1037
AN:
136404
Hom.:
9
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0230
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00422
Gnomad ASJ
AF:
0.00250
Gnomad EAS
AF:
0.00104
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00231
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00139
Gnomad OTH
AF:
0.00330
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.00766
AC:
1045
AN:
136438
Hom.:
9
Cov.:
32
AF XY:
0.00753
AC XY:
497
AN XY:
65990
show subpopulations
Gnomad4 AFR
AF:
0.0232
Gnomad4 AMR
AF:
0.00415
Gnomad4 ASJ
AF:
0.00250
Gnomad4 EAS
AF:
0.00104
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00231
Gnomad4 NFE
AF:
0.00139
Gnomad4 OTH
AF:
0.00327

ClinVar

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

Submissions by phenotype

Hyperinsulinism, Dominant Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

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: rs886045060; hg19: chr1-113455427; API