Variant chr9-137231952-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001177316.2(SLC34A3):c.86-120C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0133 in 1,169,576 control chromosomes in the GnomAD database, including 141 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.010 ( 10 hom., cov: 33)

Exomes 𝑓: 0.014 ( 131 hom. )

Consequence

SLC34A3
NM_001177316.2 intron

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.19

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 9-137231952-C-T is Benign according to our data. Variant chr9-137231952-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1213253.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-137231952-C-T is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0102 (1547/152344) while in subpopulation NFE AF= 0.0166 (1132/68026). AF 95% confidence interval is 0.0158. There are 10 homozygotes in gnomad4. There are 738 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC34A3	NM_001177316.2 linkuse as main transcript	c.86-120C>T		intron_variant		ENST00000673835.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC34A3	ENST00000673835.1 linkuse as main transcript	c.86-120C>T		intron_variant			NM_001177316.2	P1

Frequencies

GnomAD3 genomes

AF:

0.0102

AC:

1551

AN:

152226

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00256

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.00497

Gnomad ASJ

AF:

0.0320

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00807

Gnomad FIN

AF:

0.00386

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0166

Gnomad OTH

AF:

0.0119

GnomAD4 exome

AF:

0.0138

AC:

14026

AN:

1017232

Hom.:

131

Cov.:

AF XY:

0.0137

AC XY:

7168

AN XY:

525130

show subpopulations

Gnomad4 AFR exome

AF:

0.00221

Gnomad4 AMR exome

AF:

0.00528

Gnomad4 ASJ exome

AF:

0.0304

Gnomad4 EAS exome

AF:

0.0000265

Gnomad4 SAS exome

AF:

0.00821

Gnomad4 FIN exome

AF:

0.00506

Gnomad4 NFE exome

AF:

0.0162

Gnomad4 OTH exome

AF:

0.0137

GnomAD4 genome

AF:

0.0102

AC:

1547

AN:

152344

Hom.:

Cov.:

AF XY:

0.00991

AC XY:

738

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.00255

Gnomad4 AMR

AF:

0.00496

Gnomad4 ASJ

AF:

0.0320

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00766

Gnomad4 FIN

AF:

0.00386

Gnomad4 NFE

AF:

0.0166

Gnomad4 OTH

AF:

0.0113

Alfa

AF:

0.0144

Hom.:

Bravo

AF:

0.00972

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.7

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.16

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