NM_001177316.2:c.1094-10T>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001177316.2(SLC34A3):c.1094-10T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,598,284 control chromosomes in the GnomAD database, including 11,360 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1108 hom., cov: 32)

Exomes 𝑓: 0.11 ( 10252 hom. )

Consequence

SLC34A3
NM_001177316.2 intron

Scores

Splicing: ADA: 0.1561

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -3.37

Publications

7 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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 9-137234406-T-A is Benign according to our data. Variant chr9-137234406-T-A is described in ClinVar as Benign. ClinVar VariationId is 504912.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC34A3	NM_001177316.2 link	c.1094-10T>A		intron_variant	Intron 10 of 12	ENST00000673835.1	NP_001170787.2	Q8N130

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC34A3	ENST00000673835.1 link	c.1094-10T>A	intron_variant	Intron 10 of 12		NM_001177316.2	ENSP00000501114.1	Q8N130
SLC34A3	ENST00000361134.2 link	c.1094-10T>A	intron_variant	Intron 10 of 12	2		ENSP00000355353.2	Q8N130
SLC34A3	ENST00000538474.5 link	c.1094-10T>A	intron_variant	Intron 10 of 12	5		ENSP00000442397.1	Q8N130
SLC34A3	ENST00000673865.1 link	c.*164T>A	downstream_gene_variant				ENSP00000501101.1	A0A669KB63

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17569

AN:

151842

Hom.:

1111

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.0582

Gnomad AMR

AF:

0.0732

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.207

Gnomad SAS

AF:

0.179

Gnomad FIN

AF:

0.0966

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.128

GnomAD2 exomes

AF:

0.127

AC:

29165

AN:

230068

AF XY:

0.133

show subpopulations

Gnomad AFR exome

AF:

0.114

Gnomad AMR exome

AF:

0.0617

Gnomad ASJ exome

AF:

0.137

Gnomad EAS exome

AF:

0.219

Gnomad FIN exome

AF:

0.110

Gnomad NFE exome

AF:

0.116

Gnomad OTH exome

AF:

0.138

GnomAD4 exome

AF:

0.114

AC:

164536

AN:

1446324

Hom.:

10252

Cov.:

AF XY:

0.117

AC XY:

84173

AN XY:

719896

show subpopulations

African (AFR)

AF:

0.114

AC:

3809

AN:

33442

American (AMR)

AF:

0.0661

AC:

2950

AN:

44638

Ashkenazi Jewish (ASJ)

AF:

0.137

AC:

3567

AN:

26078

East Asian (EAS)

AF:

0.195

AC:

7714

AN:

39648

South Asian (SAS)

AF:

0.188

AC:

16192

AN:

86178

European-Finnish (FIN)

AF:

0.107

AC:

4194

AN:

39160

Middle Eastern (MID)

AF:

0.202

AC:

1163

AN:

5764

European-Non Finnish (NFE)

AF:

0.106

AC:

117729

AN:

1111246

Other (OTH)

AF:

0.120

AC:

7218

AN:

60170

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

8476

16952

25428

33904

42380

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4280

8560

12840

17120

21400

<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:

0.116

AC:

17555

AN:

151960

Hom.:

1108

Cov.:

AF XY:

0.115

AC XY:

8574

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.115

AC:

4754

AN:

41452

American (AMR)

AF:

0.0731

AC:

1117

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.141

AC:

489

AN:

3468

East Asian (EAS)

AF:

0.206

AC:

1058

AN:

5130

South Asian (SAS)

AF:

0.179

AC:

859

AN:

4808

European-Finnish (FIN)

AF:

0.0966

AC:

1023

AN:

10588

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.116

AC:

7873

AN:

67912

Other (OTH)

AF:

0.128

AC:

270

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

781

1563

2344

3126

3907

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

204

408

612

816

1020

<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:

0.125

Hom.:

239

Bravo

AF:

0.113

Asia WGS

AF:

0.183

AC:

635

AN:

3478

ClinVar

Significance: 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:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Aug 16, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:2

Mar 21, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

c.1094-10T>A in intron 10 of SLC34A3: This variant is not expected to have clini cal significance because it has been identified in 22.86% (1865/8158) of East As ian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinst itute.org; dbSNP rs35535797). -

Aug 22, 2018

Eurofins Ntd Llc (ga)

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

-0.81

CADD

Benign

6.6

(source)

DANN

Benign

0.85

PhyloP100

-3.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.16

dbscSNV1_RF

Benign

0.35

SpliceAI score (max)

0.080

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