Variant 17-7041768-G-T details in Genebe, Genetics Data Aggregator

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

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]

SLC16A11 links:

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
SLC16A11	NM_001370549.1 link	c.1255C>A	p.Pro419Thr	missense_variant	5/5	ENST00000574600.3	NP_001357478.1
SLC16A11	NM_153357.3 link	c.1255C>A	p.Pro419Thr	missense_variant	4/4		NP_699188.2	Q8NCK7
SLC16A11	NM_001370553.1 link	c.*163C>A		3_prime_UTR_variant	4/4		NP_001357482.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLC16A11	ENST00000574600.3 link	c.1255C>A	p.Pro419Thr	missense_variant	5/5	3	NM_001370549.1	ENSP00000460927.2	I3L431
SLC16A11	ENST00000573338.1 link	n.818C>A		non_coding_transcript_exon_variant	2/2	1
SLC16A11	ENST00000662352.3 link	c.1255C>A	p.Pro419Thr	missense_variant	4/4			ENSP00000499634.1	I3L431
SLC16A11	ENST00000673828 link	c.*163C>A		3_prime_UTR_variant	4/4			ENSP00000501313.1	A0A669KBK5

Frequencies

GnomAD3 genomes

AF:

0.0251

AC:

3814

AN:

152054

Hom.:

269

Cov.:

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.:

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.:

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.:

Bravo

AF:

0.0383

TwinsUK

AF:

0.00539

AC:

ALSPAC

AF:

0.00986

AC:

ESP6500AA

AF:

0.00386

AC:

ESP6500EA

AF:

0.00746

AC:

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

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0060

T;.

Eigen

Benign

0.16

Eigen_PC

Benign

0.20

FATHMM_MKL

Uncertain

0.83

LIST_S2

Benign

0.80

T;T

MetaRNN

Benign

0.0015

T;T

MetaSVM

Benign

-0.78

MutationAssessor

Benign

1.0

L;.

PrimateAI

Benign

0.40

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

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over