rs35535797

Variant names:

• chr9-137234406-T-A
• rs35535797
• NM_001177316.2:c.1094-10T>A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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

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]

ACMG classification

Verdict is Benign. Variant got -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 id 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	c.1094-10T>A		intron_variant	Intron 10 of 12	ENST00000673835.1	NP_001170787.2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17569 AN: 151842 Hom.: 1111 Cov.: 32

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

GnomAD3 exomes AF: 0.127 AC: 29165 AN: 230068 Hom.: 2113 AF XY: 0.133 AC XY: 16852 AN XY: 127150

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 SAS exome AF: 0.191

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.: 36 AF XY: 0.117 AC XY: 84173 AN XY: 719896

Gnomad4 AFR exome AF: 0.114

Gnomad4 AMR exome AF: 0.0661

Gnomad4 ASJ exome AF: 0.137

Gnomad4 EAS exome AF: 0.195

Gnomad4 SAS exome AF: 0.188

Gnomad4 FIN exome AF: 0.107

Gnomad4 NFE exome AF: 0.106

Gnomad4 OTH exome AF: 0.120

GnomAD4 genome AF: 0.116 AC: 17555 AN: 151960 Hom.: 1108 Cov.: 32 AF XY: 0.115 AC XY: 8574 AN XY: 74262

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0731

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.0966

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.128

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

Submissions by phenotype

not provided Benign:3

Aug 16, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: 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

- -

not specified Benign:2

Aug 22, 2018

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.6
DANN	Benign	0.85

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

LitVar

Other links and lift over

dbSNP: rs35535797; hg19: chr9-140128858;