NM_001370549.1:c.308A>G

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001370549.1(SLC16A11):c.308A>G(p.Asp103Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0395 in 1,612,368 control chromosomes in the GnomAD database, including 7,567 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D103Y) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.12 ( 2819 hom., cov: 33)

Exomes 𝑓: 0.031 ( 4748 hom. )

Consequence

SLC16A11
NM_001370549.1 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.276

Publications

36 publications found

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:

LOC124903909 (HGNC:):

LOC124903909 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0112018585).

BP6

Variant 17-7042968-T-C is Benign according to our data. Variant chr17-7042968-T-C is described in ClinVar as Benign. ClinVar VariationId is 1182780.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370549.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
SLC16A11	NM_001370549.1	MANE Select	c.308A>G	p.Asp103Gly	missense	Exon 3 of 5	NP_001357478.1
SLC16A11	NM_153357.3		c.308A>G	p.Asp103Gly	missense	Exon 2 of 4	NP_699188.2
SLC16A11	NM_001370553.1		c.308A>G	p.Asp103Gly	missense	Exon 3 of 4	NP_001357482.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
SLC16A11	ENST00000574600.3	TSL:3 MANE Select	c.308A>G	p.Asp103Gly	missense	Exon 3 of 5	ENSP00000460927.2
SLC16A11	ENST00000573338.1	TSL:1	n.639A>G		non_coding_transcript_exon	Exon 1 of 2
SLC16A11	ENST00000662352.3		c.308A>G	p.Asp103Gly	missense	Exon 2 of 4	ENSP00000499634.1

Frequencies

GnomAD3 genomes

AF:

0.123

AC:

18704

AN:

152090

Hom.:

2796

Cov.:

show subpopulations

Gnomad AFR

AF:

0.333

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.193

Gnomad ASJ

AF:

0.0377

Gnomad EAS

AF:

0.0948

Gnomad SAS

AF:

0.0120

Gnomad FIN

AF:

0.0214

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0118

Gnomad OTH

AF:

0.111

GnomAD2 exomes

AF:

0.0819

AC:

20111

AN:

245446

AF XY:

0.0640

show subpopulations

Gnomad AFR exome

AF:

0.340

Gnomad AMR exome

AF:

0.311

Gnomad ASJ exome

AF:

0.0376

Gnomad EAS exome

AF:

0.0965

Gnomad FIN exome

AF:

0.0209

Gnomad NFE exome

AF:

0.0106

Gnomad OTH exome

AF:

0.0595

GnomAD4 exome

AF:

0.0308

AC:

44923

AN:

1460160

Hom.:

4748

Cov.:

AF XY:

0.0278

AC XY:

20225

AN XY:

726342

show subpopulations

African (AFR)

AF:

0.345

AC:

11549

AN:

33456

American (AMR)

AF:

0.301

AC:

13362

AN:

44452

Ashkenazi Jewish (ASJ)

AF:

0.0380

AC:

991

AN:

26090

East Asian (EAS)

AF:

0.0862

AC:

3419

AN:

39668

South Asian (SAS)

AF:

0.00636

AC:

547

AN:

86066

European-Finnish (FIN)

AF:

0.0189

AC:

997

AN:

52684

Middle Eastern (MID)

AF:

0.0330

AC:

190

AN:

5766

European-Non Finnish (NFE)

AF:

0.00998

AC:

11092

AN:

1111640

Other (OTH)

AF:

0.0460

AC:

2776

AN:

60338

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

2212

4424

6636

8848

11060

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

764

1528

2292

3056

3820

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.123

AC:

18778

AN:

152208

Hom.:

2819

Cov.:

AF XY:

0.123

AC XY:

9123

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.334

AC:

13868

AN:

41522

American (AMR)

AF:

0.193

AC:

2959

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0377

AC:

131

AN:

3472

East Asian (EAS)

AF:

0.0945

AC:

487

AN:

5156

South Asian (SAS)

AF:

0.0120

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0214

AC:

227

AN:

10612

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0118

AC:

802

AN:

68000

Other (OTH)

AF:

0.109

AC:

231

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

681

1362

2043

2724

3405

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

170

340

510

680

850

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0480

Hom.:

3712

Bravo

AF:

0.151

TwinsUK

AF:

0.00890

AC:

ALSPAC

AF:

0.0127

AC:

ESP6500AA

AF:

0.305

AC:

1343

ESP6500EA

AF:

0.0126

AC:

108

ExAC

AF:

0.0753

AC:

9126

Asia WGS

AF:

0.0650

AC:

225

AN:

3478

EpiCase

AF:

0.0129

EpiControl

AF:

0.0130

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Feb 18, 2020

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is associated with the following publications: (PMID: 31118516)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.72

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.052

Eigen

Benign

-0.64

Eigen_PC

Benign

-0.52

FATHMM_MKL

Benign

0.068

LIST_S2

Benign

0.12

MetaRNN

Benign

0.011

MetaSVM

Benign

-0.99

MutationAssessor

Benign

-0.26

PhyloP100

0.28

PrimateAI

Benign

0.41

PROVEAN

Benign

-0.28

REVEL

Benign

0.11

Sift

Benign

0.044

Sift4G

Uncertain

0.022

Polyphen

0.0010

Vest4

0.055

MPC

0.43

ClinPred

0.0049

GERP RS

5.2

Varity_R

0.080

gMVP

0.37

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over