rs28591989

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001177316.2(SLC34A3):c.*14A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 1,534,196 control chromosomes in the GnomAD database, including 129,849 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 12188 hom., cov: 33)

Exomes 𝑓: 0.41 ( 117661 hom. )

Consequence

SLC34A3
NM_001177316.2 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -4.56

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 9-137236430-A-C is Benign according to our data. Variant chr9-137236430-A-C is described in ClinVar as [Benign]. Clinvar id is 194276.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-137236430-A-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC34A3	NM_001177316.2 link	c.*14A>C		3_prime_UTR_variant	Exon 13 of 13	ENST00000673835.1	NP_001170787.2	Q8N130

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC34A3	ENST00000673835.1 link	c.*14A>C	3_prime_UTR_variant	Exon 13 of 13		NM_001177316.2	ENSP00000501114.1	Q8N130
SLC34A3	ENST00000361134.2 link	c.*14A>C	3_prime_UTR_variant	Exon 13 of 13	2		ENSP00000355353.2	Q8N130
SLC34A3	ENST00000538474.5 link	c.*14A>C	3_prime_UTR_variant	Exon 13 of 13	5		ENSP00000442397.1	Q8N130

Frequencies

GnomAD3 genomes

AF:

0.396

AC:

60144

AN:

151946

Hom.:

12178

Cov.:

show subpopulations

Gnomad AFR

AF:

0.417

Gnomad AMI

AF:

0.456

Gnomad AMR

AF:

0.385

Gnomad ASJ

AF:

0.437

Gnomad EAS

AF:

0.150

Gnomad SAS

AF:

0.358

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.420

Gnomad OTH

AF:

0.386

GnomAD3 exomes

AF:

0.380

AC:

54111

AN:

142348

Hom.:

10770

AF XY:

0.377

AC XY:

28701

AN XY:

76218

show subpopulations

Gnomad AFR exome

AF:

0.407

Gnomad AMR exome

AF:

0.410

Gnomad ASJ exome

AF:

0.428

Gnomad EAS exome

AF:

0.146

Gnomad SAS exome

AF:

0.356

Gnomad FIN exome

AF:

0.287

Gnomad NFE exome

AF:

0.421

Gnomad OTH exome

AF:

0.386

GnomAD4 exome

AF:

0.409

AC:

565204

AN:

1382132

Hom.:

117661

Cov.:

AF XY:

0.408

AC XY:

278301

AN XY:

682268

show subpopulations

Gnomad4 AFR exome

AF:

0.421

Gnomad4 AMR exome

AF:

0.402

Gnomad4 ASJ exome

AF:

0.427

Gnomad4 EAS exome

AF:

0.162

Gnomad4 SAS exome

AF:

0.355

Gnomad4 FIN exome

AF:

0.294

Gnomad4 NFE exome

AF:

0.426

Gnomad4 OTH exome

AF:

0.390

GnomAD4 genome

AF:

0.396

AC:

60176

AN:

152064

Hom.:

12188

Cov.:

AF XY:

0.386

AC XY:

28722

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.417

Gnomad4 AMR

AF:

0.384

Gnomad4 ASJ

AF:

0.437

Gnomad4 EAS

AF:

0.150

Gnomad4 SAS

AF:

0.358

Gnomad4 FIN

AF:

0.295

Gnomad4 NFE

AF:

0.420

Gnomad4 OTH

AF:

0.382

Alfa

AF:

0.319

Hom.:

1290

Bravo

AF:

0.405

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Dec 09, 2014

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:3

Aug 30, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 14, 2016

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: The SLC34A3 c.*14A>C variant is located in the 3' UTR at a non-conserved nucleotide. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 7130/17986 (1/2, 1453 homozygotes), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic SLC34A3 variant of 1/894. A reputable clinical laboratory cites the variant as benign. Therefore, taking all available lines of evidence into consideration, the variant of interest is classifed as Benign. -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.22

DANN

Benign

0.50

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