Variant rs1143672 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_021082.4(SLC15A2):c.1526G>A(p.Arg509Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 1,612,066 control chromosomes in the GnomAD database, including 171,172 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.45 ( 15684 hom., cov: 32)

Exomes 𝑓: 0.46 ( 155488 hom. )

Consequence

SLC15A2
NM_021082.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.117

Variant links:

Genes affected

SLC15A2 (HGNC:10921): (solute carrier family 15 member 2) The mammalian kidney expresses a proton-coupled peptide transporter that is responsible for the absorption of small peptides, as well as beta-lactam antibiotics and other peptide-like drugs, from the tubular filtrate. This transporter, SLC15A2, belongs to the same gene family as SLC15A1 (MIM 600544), the proton-coupled peptide transporter found in the small intestine (Liu et al, 1995 [PubMed 7756356]).[supplied by OMIM, Feb 2011]

SLC15A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=3.3310764E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SLC15A2	NM_021082.4 linkuse as main transcript	c.1526G>A	p.Arg509Lys	missense_variant	17/22	ENST00000489711.6
SLC15A2	NM_001145998.2 linkuse as main transcript	c.1433G>A	p.Arg478Lys	missense_variant	16/21
SLC15A2	XM_005247722.4 linkuse as main transcript	c.1526G>A	p.Arg509Lys	missense_variant	17/21
SLC15A2	XM_006713736.4 linkuse as main transcript	c.1526G>A	p.Arg509Lys	missense_variant	17/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC15A2	ENST00000489711.6 linkuse as main transcript	c.1526G>A	p.Arg509Lys	missense_variant	17/22	1	NM_021082.4	P1	Q16348-1
SLC15A2	ENST00000295605.6 linkuse as main transcript	c.1433G>A	p.Arg478Lys	missense_variant	16/21	2			Q16348-2
SLC15A2	ENST00000465060.1 linkuse as main transcript	n.449G>A		non_coding_transcript_exon_variant	3/4	3

Frequencies

GnomAD3 genomes

AF:

0.446

AC:

67819

AN:

151936

Hom.:

15674

Cov.:

show subpopulations

Gnomad AFR

AF:

0.484

Gnomad AMI

AF:

0.504

Gnomad AMR

AF:

0.308

Gnomad ASJ

AF:

0.393

Gnomad EAS

AF:

0.693

Gnomad SAS

AF:

0.305

Gnomad FIN

AF:

0.405

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.456

Gnomad OTH

AF:

0.396

GnomAD3 exomes

AF:

0.419

AC:

105179

AN:

250802

Hom.:

23978

AF XY:

0.417

AC XY:

56465

AN XY:

135534

show subpopulations

Gnomad AFR exome

AF:

0.485

Gnomad AMR exome

AF:

0.241

Gnomad ASJ exome

AF:

0.379

Gnomad EAS exome

AF:

0.717

Gnomad SAS exome

AF:

0.299

Gnomad FIN exome

AF:

0.409

Gnomad NFE exome

AF:

0.455

Gnomad OTH exome

AF:

0.393

GnomAD4 exome

AF:

0.455

AC:

664413

AN:

1460012

Hom.:

155488

Cov.:

AF XY:

0.450

AC XY:

326778

AN XY:

726326

show subpopulations

Gnomad4 AFR exome

AF:

0.487

Gnomad4 AMR exome

AF:

0.250

Gnomad4 ASJ exome

AF:

0.380

Gnomad4 EAS exome

AF:

0.723

Gnomad4 SAS exome

AF:

0.303

Gnomad4 FIN exome

AF:

0.410

Gnomad4 NFE exome

AF:

0.470

Gnomad4 OTH exome

AF:

0.436

GnomAD4 genome

AF:

0.446

AC:

67858

AN:

152054

Hom.:

15684

Cov.:

AF XY:

0.437

AC XY:

32503

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.483

Gnomad4 AMR

AF:

0.307

Gnomad4 ASJ

AF:

0.393

Gnomad4 EAS

AF:

0.693

Gnomad4 SAS

AF:

0.305

Gnomad4 FIN

AF:

0.405

Gnomad4 NFE

AF:

0.456

Gnomad4 OTH

AF:

0.397

Alfa

AF:

0.455

Hom.:

27815

Bravo

AF:

0.447

TwinsUK

AF:

0.471

AC:

1747

ALSPAC

AF:

0.463

AC:

1786

ESP6500AA

AF:

0.488

AC:

2150

ESP6500EA

AF:

0.454

AC:

3904

ExAC

AF:

0.425

AC:

51642

Asia WGS

AF:

0.461

AC:

1602

AN:

3478

EpiCase

AF:

0.444

EpiControl

AF:

0.442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.064

BayesDel_addAF

Benign

-0.81

BayesDel_noAF

Benign

-0.79

CADD

Benign

6.2

DANN

Benign

0.25

DEOGEN2

Benign

0.070

T;.

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.0032

LIST_S2

Benign

0.057

T;T

MetaRNN

Benign

0.0000033

T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

-2.2

N;.

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.33

PROVEAN

Benign

2.6

N;N

REVEL

Benign

0.053

Sift

Benign

1.0

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;.

Vest4

0.0040

MPC

0.076

ClinPred

0.0026

GERP RS

-2.8

Varity_R

0.050

gMVP

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.15

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