9-137234125-G-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001177316.2(SLC34A3):c.942G>C(p.Ala314Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 1,588,666 control chromosomes in the GnomAD database, including 285 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0090 ( 18 hom., cov: 31)

Exomes 𝑓: 0.011 ( 267 hom. )

Consequence

SLC34A3
NM_001177316.2 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.52

Publications

3 publications found

Variant links:

Genes affected

SLC34A3 (HGNC:20305): (solute carrier family 34 member 3) This gene encodes a member of SLC34A transporter family of proteins, and is expressed primarily in the kidney. It is involved in transporting phosphate into cells via sodium cotransport in the renal brush border membrane, and contributes to the maintenance of inorganic phosphate concentration in the kidney. Mutations in this gene are associated with hereditary hypophosphatemic rickets with hypercalciuria. Alternatively spliced transcript variants varying in the 5' UTR have been found for this gene.[provided by RefSeq, Apr 2010]

SLC34A3 Gene-Disease associations (from GenCC):

hereditary hypophosphatemic rickets with hypercalciuria
Inheritance: SD, AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae)

SLC34A3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 9-137234125-G-C is Benign according to our data. Variant chr9-137234125-G-C is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 1169030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.52 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC34A3	NM_001177316.2 link	c.942G>C	p.Ala314Ala	synonymous_variant	Exon 10 of 13	ENST00000673835.1	NP_001170787.2	Q8N130

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC34A3	ENST00000673835.1 link	c.942G>C	p.Ala314Ala	synonymous_variant	Exon 10 of 13		NM_001177316.2	ENSP00000501114.1	Q8N130
SLC34A3	ENST00000361134.2 link	c.942G>C	p.Ala314Ala	synonymous_variant	Exon 10 of 13	2		ENSP00000355353.2	Q8N130
SLC34A3	ENST00000538474.5 link	c.942G>C	p.Ala314Ala	synonymous_variant	Exon 10 of 13	5		ENSP00000442397.1	Q8N130
SLC34A3	ENST00000673865.1 link	c.942G>C	p.Ala314Ala	synonymous_variant	Exon 10 of 10			ENSP00000501101.1	A0A669KB63

Frequencies

GnomAD3 genomes

AF:

0.00902

AC:

1353

AN:

150056

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00222

Gnomad AMI

AF:

0.0198

Gnomad AMR

AF:

0.00385

Gnomad ASJ

AF:

0.0369

Gnomad EAS

AF:

0.0560

Gnomad SAS

AF:

0.0457

Gnomad FIN

AF:

0.00594

Gnomad MID

AF:

0.0160

Gnomad NFE

AF:

0.00699

Gnomad OTH

AF:

0.00975

GnomAD2 exomes

AF:

0.0160

AC:

3500

AN:

218422

AF XY:

0.0178

show subpopulations

Gnomad AFR exome

AF:

0.00144

Gnomad AMR exome

AF:

0.00373

Gnomad ASJ exome

AF:

0.0329

Gnomad EAS exome

AF:

0.0467

Gnomad FIN exome

AF:

0.00622

Gnomad NFE exome

AF:

0.00742

Gnomad OTH exome

AF:

0.0170

GnomAD4 exome

AF:

0.0106

AC:

15272

AN:

1438494

Hom.:

267

Cov.:

AF XY:

0.0120

AC XY:

8588

AN XY:

715010

show subpopulations

African (AFR)

AF:

0.00195

AC:

AN:

33312

American (AMR)

AF:

0.00421

AC:

184

AN:

43746

Ashkenazi Jewish (ASJ)

AF:

0.0358

AC:

928

AN:

25886

East Asian (EAS)

AF:

0.0450

AC:

1763

AN:

39140

South Asian (SAS)

AF:

0.0506

AC:

4280

AN:

84558

European-Finnish (FIN)

AF:

0.00869

AC:

347

AN:

39918

Middle Eastern (MID)

AF:

0.0384

AC:

189

AN:

4922

European-Non Finnish (NFE)

AF:

0.00595

AC:

6593

AN:

1107274

Other (OTH)

AF:

0.0155

AC:

923

AN:

59738

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

912

1824

2737

3649

4561

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

286

572

858

1144

1430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00902

AC:

1354

AN:

150172

Hom.:

Cov.:

AF XY:

0.00980

AC XY:

718

AN XY:

73242

show subpopulations

African (AFR)

AF:

0.00224

AC:

AN:

40620

American (AMR)

AF:

0.00384

AC:

AN:

15098

Ashkenazi Jewish (ASJ)

AF:

0.0369

AC:

128

AN:

3470

East Asian (EAS)

AF:

0.0561

AC:

283

AN:

5046

South Asian (SAS)

AF:

0.0458

AC:

217

AN:

4740

European-Finnish (FIN)

AF:

0.00594

AC:

AN:

10270

Middle Eastern (MID)

AF:

0.0171

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00699

AC:

473

AN:

67652

Other (OTH)

AF:

0.00963

AC:

AN:

2076

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

110

164

219

274

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00931

Hom.:

Bravo

AF:

0.00776

Asia WGS

AF:

0.0440

AC:

154

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Mar 29, 2021

GeneDx

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Autosomal recessive hypophosphatemic bone disease

Benign:2

Jul 27, 2021

Fulgent Genetics, Fulgent Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Nov 19, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.0

(source)

DANN

Benign

0.44

PhyloP100

-1.5

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over