Variant 5-151316979-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_181776.3(SLC36A2):c.1290G>A(p.Thr430Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 1,613,262 control chromosomes in the GnomAD database, including 259,998 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.58 ( 26129 hom., cov: 30)

Exomes 𝑓: 0.56 ( 233869 hom. )

Consequence

SLC36A2
NM_181776.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.98

Variant links:

Genes affected

SLC36A2 (HGNC:18762): (solute carrier family 36 member 2) This gene encodes a pH-dependent proton-coupled amino acid transporter that belongs to the amino acid auxin permease 1 protein family. The encoded protein primarily transports small amino acids such as glycine, alanine and proline. Mutations in this gene are associated with iminoglycinuria and hyperglycinuria. [provided by RefSeq, Sep 2010]

SLC36A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.22).

BP6

Variant 5-151316979-C-T is Benign according to our data. Variant chr5-151316979-C-T is described in ClinVar as [Benign]. Clinvar id is 1245781.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-151316979-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.98 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC36A2	NM_181776.3 linkuse as main transcript	c.1290G>A	p.Thr430Thr	synonymous_variant	10/10	ENST00000335244.9	NP_861441.2	Q495M3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC36A2	ENST00000335244.9 linkuse as main transcript	c.1290G>A	p.Thr430Thr	synonymous_variant	10/10	1	NM_181776.3	ENSP00000334223.4		Q495M3-1

Frequencies

GnomAD3 genomes

AF:

0.581

AC:

88055

AN:

151630

Hom.:

26110

Cov.:

show subpopulations

Gnomad AFR

AF:

0.600

Gnomad AMI

AF:

0.681

Gnomad AMR

AF:

0.657

Gnomad ASJ

AF:

0.640

Gnomad EAS

AF:

0.849

Gnomad SAS

AF:

0.730

Gnomad FIN

AF:

0.489

Gnomad MID

AF:

0.615

Gnomad NFE

AF:

0.531

Gnomad OTH

AF:

0.574

GnomAD3 exomes

AF:

0.619

AC:

155136

AN:

250826

Hom.:

49784

AF XY:

0.615

AC XY:

83343

AN XY:

135560

show subpopulations

Gnomad AFR exome

AF:

0.603

Gnomad AMR exome

AF:

0.766

Gnomad ASJ exome

AF:

0.641

Gnomad EAS exome

AF:

0.845

Gnomad SAS exome

AF:

0.715

Gnomad FIN exome

AF:

0.504

Gnomad NFE exome

AF:

0.534

Gnomad OTH exome

AF:

0.596

GnomAD4 exome

AF:

0.559

AC:

816865

AN:

1461514

Hom.:

233869

Cov.:

AF XY:

0.563

AC XY:

408981

AN XY:

727034

show subpopulations

Gnomad4 AFR exome

AF:

0.607

Gnomad4 AMR exome

AF:

0.757

Gnomad4 ASJ exome

AF:

0.640

Gnomad4 EAS exome

AF:

0.886

Gnomad4 SAS exome

AF:

0.713

Gnomad4 FIN exome

AF:

0.506

Gnomad4 NFE exome

AF:

0.525

Gnomad4 OTH exome

AF:

0.583

GnomAD4 genome

AF:

0.581

AC:

88128

AN:

151748

Hom.:

26129

Cov.:

AF XY:

0.585

AC XY:

43374

AN XY:

74122

show subpopulations

Gnomad4 AFR

AF:

0.600

Gnomad4 AMR

AF:

0.657

Gnomad4 ASJ

AF:

0.640

Gnomad4 EAS

AF:

0.849

Gnomad4 SAS

AF:

0.730

Gnomad4 FIN

AF:

0.489

Gnomad4 NFE

AF:

0.531

Gnomad4 OTH

AF:

0.574

Alfa

AF:

0.554

Hom.:

10221

Bravo

AF:

0.595

Asia WGS

AF:

0.766

AC:

2664

AN:

3478

EpiCase

AF:

0.540

EpiControl

AF:

0.544

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 30, 2024	- -

Hyperglycinuria

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.22

CADD

Benign

DANN

Benign

0.67

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over