5-177386403-C-T

Position:

chr5-177386403-C-T

Variant summary

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

The NM_003052.5(SLC34A1):c.389-20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 1,614,098 control chromosomes in the GnomAD database, including 48,103 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3656 hom., cov: 32)

Exomes 𝑓: 0.24 ( 44447 hom. )

Consequence

SLC34A1
NM_003052.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -1.28

Variant links:

Genes affected

SLC34A1 (HGNC:11019): (solute carrier family 34 member 1) Enables sodium:phosphate symporter activity. Involved in several processes, including phosphate ion homeostasis; phosphate ion transport; and response to lead ion. Located in several cellular components, including apical plasma membrane; mitotic spindle; and nuclear speck. Implicated in several diseases, including Fanconi syndrome (multiple); chronic kidney disease; hereditary hypophosphatemic rickets with hypercalciuria; hypophosphatemic nephrolithiasis/osteoporosis 1; and nephrolithiasis. [provided by Alliance of Genome Resources, Apr 2022]

SLC34A1 links:

SLC34A1 (HGNC:):

SLC34A1 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=-0.91).

BP6

Variant 5-177386403-C-T is Benign according to our data. Variant chr5-177386403-C-T is described in ClinVar as [Benign]. Clinvar id is 1168138.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177386403-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC34A1	NM_003052.5 linkuse as main transcript	c.389-20C>T		intron_variant		ENST00000324417.6	NP_003043.3	Q06495-1A0A024R7R9Q86VN6Q7Z725
SLC34A1	NM_001167579.2 linkuse as main transcript	c.389-20C>T		intron_variant			NP_001161051.1	Q06495-2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
SLC34A1	ENST00000324417.6 linkuse as main transcript	c.389-20C>T	intron_variant	1	NM_003052.5	ENSP00000321424.4	Q06495-1
SLC34A1	ENST00000512593.5 linkuse as main transcript	c.389-20C>T	intron_variant	2		ENSP00000423022.1	Q06495-2
SLC34A1	ENST00000507685.5 linkuse as main transcript	n.473-20C>T	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30515

AN:

152128

Hom.:

3652

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0740

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.227

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.159

Gnomad SAS

AF:

0.256

Gnomad FIN

AF:

0.320

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.209

GnomAD3 exomes

AF:

0.228

AC:

57263

AN:

251374

Hom.:

7124

AF XY:

0.237

AC XY:

32235

AN XY:

135876

show subpopulations

Gnomad AFR exome

AF:

0.0706

Gnomad AMR exome

AF:

0.176

Gnomad ASJ exome

AF:

0.196

Gnomad EAS exome

AF:

0.153

Gnomad SAS exome

AF:

0.270

Gnomad FIN exome

AF:

0.301

Gnomad NFE exome

AF:

0.255

Gnomad OTH exome

AF:

0.247

GnomAD4 exome

AF:

0.243

AC:

354687

AN:

1461852

Hom.:

44447

Cov.:

AF XY:

0.244

AC XY:

177600

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.0633

Gnomad4 AMR exome

AF:

0.183

Gnomad4 ASJ exome

AF:

0.199

Gnomad4 EAS exome

AF:

0.208

Gnomad4 SAS exome

AF:

0.270

Gnomad4 FIN exome

AF:

0.303

Gnomad4 NFE exome

AF:

0.248

Gnomad4 OTH exome

AF:

0.228

GnomAD4 genome

AF:

0.200

AC:

30521

AN:

152246

Hom.:

3656

Cov.:

AF XY:

0.204

AC XY:

15163

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.0742

Gnomad4 AMR

AF:

0.227

Gnomad4 ASJ

AF:

0.186

Gnomad4 EAS

AF:

0.158

Gnomad4 SAS

AF:

0.257

Gnomad4 FIN

AF:

0.320

Gnomad4 NFE

AF:

0.253

Gnomad4 OTH

AF:

0.208

Alfa

AF:

0.209

Hom.:

875

Bravo

AF:

0.187

Asia WGS

AF:

0.217

AC:

759

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 16, 2018	- -

Fanconi renotubular syndrome 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Hypophosphatemic nephrolithiasis/osteoporosis 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Hypercalcemia, infantile, 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.080

DANN

Benign

0.45

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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