chr9-137231952-C-T

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

2

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

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]

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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
SLC34A3NM_001177316.2 linkuse as main transcriptc.86-120C>T intron_variant ENST00000673835.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC34A3ENST00000673835.1 linkuse as main transcriptc.86-120C>T intron_variant NM_001177316.2 P1

Frequencies

GnomAD3 genomes
AF:
0.0102
AC:
1551
AN:
152226
Hom.:
10
Cov.:
33
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.:
14
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.:
10
Cov.:
33
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.:
3
Bravo
AF:
0.00972
Asia WGS
AF:
0.00173
AC:
6
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Likely benign, criteria provided, single submitterclinical testingGeneDxDec 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.

Other links and lift over

dbSNP: rs112695368; hg19: chr9-140126404; API