Variant 5-151316937-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_181776.3(SLC36A2):c.1332C>T(p.Asp444Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 1,613,314 control chromosomes in the GnomAD database, including 117,011 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 8807 hom., cov: 29)

Exomes 𝑓: 0.38 ( 108204 hom. )

Consequence

SLC36A2
NM_181776.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.10

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP6

Variant 5-151316937-G-A is Benign according to our data. Variant chr5-151316937-G-A is described in ClinVar as [Benign]. Clinvar id is 1274519.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-151316937-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.1 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.481 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.1332C>T	p.Asp444Asp	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.1332C>T	p.Asp444Asp	synonymous_variant	10/10	1	NM_181776.3	ENSP00000334223.4		Q495M3-1

Frequencies

GnomAD3 genomes

AF:

0.305

AC:

46283

AN:

151664

Hom.:

8803

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0771

Gnomad AMI

AF:

0.471

Gnomad AMR

AF:

0.489

Gnomad ASJ

AF:

0.381

Gnomad EAS

AF:

0.445

Gnomad SAS

AF:

0.421

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.373

Gnomad OTH

AF:

0.331

GnomAD3 exomes

AF:

0.397

AC:

99782

AN:

251080

Hom.:

21848

AF XY:

0.396

AC XY:

53710

AN XY:

135724

show subpopulations

Gnomad AFR exome

AF:

0.0711

Gnomad AMR exome

AF:

0.624

Gnomad ASJ exome

AF:

0.388

Gnomad EAS exome

AF:

0.445

Gnomad SAS exome

AF:

0.413

Gnomad FIN exome

AF:

0.348

Gnomad NFE exome

AF:

0.373

Gnomad OTH exome

AF:

0.407

GnomAD4 exome

AF:

0.378

AC:

553054

AN:

1461532

Hom.:

108204

Cov.:

AF XY:

0.379

AC XY:

275769

AN XY:

727084

show subpopulations

Gnomad4 AFR exome

AF:

0.0675

Gnomad4 AMR exome

AF:

0.610

Gnomad4 ASJ exome

AF:

0.391

Gnomad4 EAS exome

AF:

0.442

Gnomad4 SAS exome

AF:

0.417

Gnomad4 FIN exome

AF:

0.351

Gnomad4 NFE exome

AF:

0.374

Gnomad4 OTH exome

AF:

0.381

GnomAD4 genome

AF:

0.305

AC:

46289

AN:

151782

Hom.:

8807

Cov.:

AF XY:

0.311

AC XY:

23025

AN XY:

74138

show subpopulations

Gnomad4 AFR

AF:

0.0769

Gnomad4 AMR

AF:

0.490

Gnomad4 ASJ

AF:

0.381

Gnomad4 EAS

AF:

0.445

Gnomad4 SAS

AF:

0.421

Gnomad4 FIN

AF:

0.332

Gnomad4 NFE

AF:

0.373

Gnomad4 OTH

AF:

0.329

Alfa

AF:

0.343

Hom.:

4927

Bravo

AF:

0.307

Asia WGS

AF:

0.413

AC:

1437

AN:

3478

EpiCase

AF:

0.374

EpiControl

AF:

0.378

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

7.3

DANN

Benign

0.58

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