17-7041768-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001370549.1(SLC16A11):​c.1255C>A​(p.Pro419Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0186 in 1,613,562 control chromosomes in the GnomAD database, including 2,566 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.025 ( 269 hom., cov: 32)
Exomes 𝑓: 0.018 ( 2297 hom. )

Consequence

SLC16A11
NM_001370549.1 missense

Scores

3
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10
Variant links:
Genes affected
SLC16A11 (HGNC:23093): (solute carrier family 16 member 11) Enables pyruvate transmembrane transporter activity. Involved in lipid metabolic process. Located in endoplasmic reticulum membrane and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0015069842).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC16A11NM_001370549.1 linkc.1255C>A p.Pro419Thr missense_variant 5/5 ENST00000574600.3 NP_001357478.1
SLC16A11NM_153357.3 linkc.1255C>A p.Pro419Thr missense_variant 4/4 NP_699188.2 Q8NCK7
SLC16A11NM_001370553.1 linkc.*163C>A 3_prime_UTR_variant 4/4 NP_001357482.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC16A11ENST00000574600.3 linkc.1255C>A p.Pro419Thr missense_variant 5/53 NM_001370549.1 ENSP00000460927.2 I3L431
SLC16A11ENST00000573338.1 linkn.818C>A non_coding_transcript_exon_variant 2/21
SLC16A11ENST00000662352.3 linkc.1255C>A p.Pro419Thr missense_variant 4/4 ENSP00000499634.1 I3L431
SLC16A11ENST00000673828 linkc.*163C>A 3_prime_UTR_variant 4/4 ENSP00000501313.1 A0A669KBK5

Frequencies

GnomAD3 genomes
AF:
0.0251
AC:
3814
AN:
152054
Hom.:
269
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00476
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.150
Gnomad ASJ
AF:
0.00778
Gnomad EAS
AF:
0.0967
Gnomad SAS
AF:
0.00787
Gnomad FIN
AF:
0.0213
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00704
Gnomad OTH
AF:
0.0311
GnomAD3 exomes
AF:
0.0543
AC:
13523
AN:
248848
Hom.:
1816
AF XY:
0.0430
AC XY:
5815
AN XY:
135292
show subpopulations
Gnomad AFR exome
AF:
0.00499
Gnomad AMR exome
AF:
0.293
Gnomad ASJ exome
AF:
0.00941
Gnomad EAS exome
AF:
0.0974
Gnomad SAS exome
AF:
0.00425
Gnomad FIN exome
AF:
0.0208
Gnomad NFE exome
AF:
0.00600
Gnomad OTH exome
AF:
0.0402
GnomAD4 exome
AF:
0.0180
AC:
26265
AN:
1461390
Hom.:
2297
Cov.:
32
AF XY:
0.0164
AC XY:
11913
AN XY:
726984
show subpopulations
Gnomad4 AFR exome
AF:
0.00311
Gnomad4 AMR exome
AF:
0.280
Gnomad4 ASJ exome
AF:
0.00911
Gnomad4 EAS exome
AF:
0.0906
Gnomad4 SAS exome
AF:
0.00445
Gnomad4 FIN exome
AF:
0.0186
Gnomad4 NFE exome
AF:
0.00661
Gnomad4 OTH exome
AF:
0.0182
GnomAD4 genome
AF:
0.0251
AC:
3817
AN:
152172
Hom.:
269
Cov.:
32
AF XY:
0.0280
AC XY:
2082
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.00474
Gnomad4 AMR
AF:
0.150
Gnomad4 ASJ
AF:
0.00778
Gnomad4 EAS
AF:
0.0964
Gnomad4 SAS
AF:
0.00767
Gnomad4 FIN
AF:
0.0213
Gnomad4 NFE
AF:
0.00705
Gnomad4 OTH
AF:
0.0303
Alfa
AF:
0.00611
Hom.:
10
Bravo
AF:
0.0383
TwinsUK
AF:
0.00539
AC:
20
ALSPAC
AF:
0.00986
AC:
38
ESP6500AA
AF:
0.00386
AC:
17
ESP6500EA
AF:
0.00746
AC:
64
ExAC
AF:
0.0432
AC:
5241
Asia WGS
AF:
0.0460
AC:
160
AN:
3478
EpiCase
AF:
0.00682
EpiControl
AF:
0.00622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.069
BayesDel_addAF
Benign
-0.60
T
BayesDel_noAF
Benign
-0.50
CADD
Benign
20
DANN
Uncertain
1.0
DEOGEN2
Benign
0.0060
T;.
Eigen
Benign
0.16
Eigen_PC
Benign
0.20
FATHMM_MKL
Uncertain
0.83
D
LIST_S2
Benign
0.80
T;T
MetaRNN
Benign
0.0015
T;T
MetaSVM
Benign
-0.78
T
MutationAssessor
Benign
1.0
L;.
PrimateAI
Benign
0.40
T
PROVEAN
Benign
-0.67
N;N
REVEL
Benign
0.052
Sift
Benign
0.31
T;T
Sift4G
Uncertain
0.036
D;D
Polyphen
0.89
P;.
Vest4
0.23
MPC
1.1
ClinPred
0.017
T
GERP RS
5.1
Varity_R
0.087
gMVP
0.42

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: rs75493593; hg19: chr17-6945087; COSMIC: COSV57274354; COSMIC: COSV57274354; API