Genetic Variant SLC43A2:c.*401G>A (chr17-1575203-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152346.3(SLC43A2):c.*401G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0907 in 311,278 control chromosomes in the GnomAD database, including 1,476 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.

Frequency

Genomes: 𝑓 0.088 ( 657 hom., cov: 33)

Exomes 𝑓: 0.093 ( 819 hom. )

Consequence

SLC43A2
NM_152346.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.491

Variant links:

Genes affected

SLC43A2 (HGNC:23087): (solute carrier family 43 member 2) This gene encodes a member of the L-amino acid transporter-3 or SLC43 family of transporters. The encoded protein mediates sodium-, chloride-, and pH-independent transport of L-isomers of neutral amino acids, including leucine, phenylalanine, valine and methionine. This protein may contribute to the transfer of amino acids across the placental membrane to the fetus. [provided by RefSeq, Mar 2016]

SLC43A2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC43A2	NM_152346.3 link	c.*401G>A		3_prime_UTR_variant	Exon 14 of 14	ENST00000301335.10	NP_689559.1	Q8N370-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC43A2	ENST00000301335.10 link	c.*401G>A		3_prime_UTR_variant	Exon 14 of 14	1	NM_152346.3	ENSP00000301335.5		Q8N370-1
SLC43A2	ENST00000571650.5 link	c.*401G>A		3_prime_UTR_variant	Exon 15 of 15	1		ENSP00000461382.1		Q8N370-3

Frequencies

GnomAD3 genomes

AF:

0.0881

AC:

13406

AN:

152124

Hom.:

655

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0607

Gnomad AMI

AF:

0.0538

Gnomad AMR

AF:

0.161

Gnomad ASJ

AF:

0.0599

Gnomad EAS

AF:

0.0823

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.0821

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0888

Gnomad OTH

AF:

0.0909

GnomAD4 exome

AF:

0.0931

AC:

14803

AN:

159036

Hom.:

819

Cov.:

AF XY:

0.0989

AC XY:

8577

AN XY:

86724

show subpopulations

African (AFR)

AF:

0.0568

AC:

183

AN:

3220

American (AMR)

AF:

0.180

AC:

914

AN:

5090

Ashkenazi Jewish (ASJ)

AF:

0.0563

AC:

210

AN:

3732

East Asian (EAS)

AF:

0.0906

AC:

386

AN:

4260

South Asian (SAS)

AF:

0.126

AC:

3869

AN:

30652

European-Finnish (FIN)

AF:

0.0753

AC:

630

AN:

8366

Middle Eastern (MID)

AF:

0.0645

AC:

AN:

620

European-Non Finnish (NFE)

AF:

0.0834

AC:

7925

AN:

95080

Other (OTH)

AF:

0.0806

AC:

646

AN:

8016

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

635

1270

1905

2540

3175

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0881

AC:

13419

AN:

152242

Hom.:

657

Cov.:

AF XY:

0.0902

AC XY:

6714

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.0609

AC:

2531

AN:

41536

American (AMR)

AF:

0.161

AC:

2461

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0599

AC:

208

AN:

3470

East Asian (EAS)

AF:

0.0823

AC:

426

AN:

5174

South Asian (SAS)

AF:

0.129

AC:

624

AN:

4828

European-Finnish (FIN)

AF:

0.0821

AC:

871

AN:

10604

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0888

AC:

6042

AN:

68010

Other (OTH)

AF:

0.0900

AC:

190

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

646

1292

1938

2584

3230

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0694

Hom.:

147

Bravo

AF:

0.0923

Asia WGS

AF:

0.111

AC:

385

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

9.5

(source)

DANN

Benign

0.79

PhyloP100

0.49

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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chr17-1575203-C-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over