Variant rs12210538 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_033125.4(SLC22A16):c.1226T>C(p.Met409Thr) variant causes a missense change. The variant allele was found at a frequency of 0.206 in 1,613,622 control chromosomes in the GnomAD database, including 37,919 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.16 ( 2501 hom., cov: 32)

Exomes 𝑓: 0.21 ( 35418 hom. )

Consequence

SLC22A16
NM_033125.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.41

Variant links:

Genes affected

SLC22A16 (HGNC:20302): (solute carrier family 22 member 16) This gene encodes a member of the organic zwitterion transporter protein family which transports carnitine. The encoded protein has also been shown to transport anticancer drugs like bleomycin (PMID: 20037140) successful treatment has been correlated with the level of activity of this transporter in tumor cells. [provided by RefSeq, Dec 2011]

SLC22A16 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=0.0019080639).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A16	NM_033125.4 linkuse as main transcript	c.1226T>C	p.Met409Thr	missense_variant	5/8	ENST00000368919.8	NP_149116.2	Q86VW1-1A0A0K0K1K9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLC22A16	ENST00000368919.8 linkuse as main transcript	c.1226T>C	p.Met409Thr	missense_variant	5/8	1	NM_033125.4	ENSP00000357915.3	Q86VW1-1
SLC22A16	ENST00000330550.8 linkuse as main transcript	c.1124T>C	p.Met375Thr	missense_variant	7/10	1		ENSP00000328583.4	Q86VW1-2
SLC22A16	ENST00000451557.5 linkuse as main transcript	c.977T>C	p.Met326Thr	missense_variant	4/7	2		ENSP00000395642.1	X6RE50
SLC22A16	ENST00000434949.5 linkuse as main transcript	c.716T>C	p.Met239Thr	missense_variant	5/5	3		ENSP00000409306.1	C9JTF8

Frequencies

GnomAD3 genomes

AF:

0.158

AC:

23988

AN:

152126

Hom.:

2500

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0413

Gnomad AMI

AF:

0.314

Gnomad AMR

AF:

0.160

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.236

Gnomad OTH

AF:

0.184

GnomAD3 exomes

AF:

0.169

AC:

42323

AN:

250846

Hom.:

4566

AF XY:

0.175

AC XY:

23727

AN XY:

135568

show subpopulations

Gnomad AFR exome

AF:

0.0381

Gnomad AMR exome

AF:

0.117

Gnomad ASJ exome

AF:

0.274

Gnomad EAS exome

AF:

0.000381

Gnomad SAS exome

AF:

0.113

Gnomad FIN exome

AF:

0.159

Gnomad NFE exome

AF:

0.236

Gnomad OTH exome

AF:

0.203

GnomAD4 exome

AF:

0.211

AC:

308501

AN:

1461378

Hom.:

35418

Cov.:

AF XY:

0.210

AC XY:

152678

AN XY:

727002

show subpopulations

Gnomad4 AFR exome

AF:

0.0374

Gnomad4 AMR exome

AF:

0.125

Gnomad4 ASJ exome

AF:

0.278

Gnomad4 EAS exome

AF:

0.000554

Gnomad4 SAS exome

AF:

0.116

Gnomad4 FIN exome

AF:

0.158

Gnomad4 NFE exome

AF:

0.236

Gnomad4 OTH exome

AF:

0.198

GnomAD4 genome

AF:

0.158

AC:

23989

AN:

152244

Hom.:

2501

Cov.:

AF XY:

0.153

AC XY:

11382

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.0412

Gnomad4 AMR

AF:

0.159

Gnomad4 ASJ

AF:

0.267

Gnomad4 EAS

AF:

0.00154

Gnomad4 SAS

AF:

0.105

Gnomad4 FIN

AF:

0.151

Gnomad4 NFE

AF:

0.236

Gnomad4 OTH

AF:

0.182

Alfa

AF:

0.223

Hom.:

9175

Bravo

AF:

0.157

TwinsUK

AF:

0.226

AC:

839

ALSPAC

AF:

0.232

AC:

896

ESP6500AA

AF:

0.0511

AC:

225

ESP6500EA

AF:

0.243

AC:

2091

ExAC

AF:

0.168

AC:

20377

Asia WGS

AF:

0.0510

AC:

179

AN:

3478

EpiCase

AF:

0.253

EpiControl

AF:

0.253

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.56

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.17

CADD

Benign

DANN

Benign

0.93

DEOGEN2

Benign

0.27

.;T;.;.

Eigen

Uncertain

0.28

Eigen_PC

Benign

0.16

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.74

T;T;T;T

MetaRNN

Benign

0.0019

T;T;T;T

MetaSVM

Uncertain

-0.14

MutationAssessor

Uncertain

2.1

.;M;.;.

PrimateAI

Benign

0.39

PROVEAN

Uncertain

-4.2

D;D;D;D

REVEL

Uncertain

0.35

Sift

Uncertain

0.0040

D;D;D;D

Sift4G

Uncertain

0.0060

D;D;D;D

Polyphen

0.96, 0.95

.;D;P;.

Vest4

0.46, 0.29

MPC

0.095

ClinPred

0.049

GERP RS

5.0

Varity_R

0.64

gMVP

0.85

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