Variant 4-25667908-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_006424.3(SLC34A2):c.552T>C(p.Ile184=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 1,612,818 control chromosomes in the GnomAD database, including 788 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.022 ( 78 hom., cov: 32)

Exomes 𝑓: 0.028 ( 710 hom. )

Consequence

SLC34A2
NM_006424.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.122

Variant links:

Genes affected

SLC34A2 (HGNC:11020): (solute carrier family 34 member 2) The protein encoded by this gene is a pH-sensitive sodium-dependent phosphate transporter. Phosphate uptake is increased at lower pH. Defects in this gene are a cause of pulmonary alveolar microlithiasis. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, May 2010]

SLC34A2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 4-25667908-T-C is Benign according to our data. Variant chr4-25667908-T-C is described in ClinVar as [Benign]. Clinvar id is 403455.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-25667908-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.122 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.022 (3346/152292) while in subpopulation NFE AF= 0.0305 (2074/68026). AF 95% confidence interval is 0.0294. There are 78 homozygotes in gnomad4. There are 1666 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 78 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SLC34A2	NM_006424.3 linkuse as main transcript	c.552T>C	p.Ile184=	synonymous_variant	6/13	ENST00000382051.8	NP_006415.3
SLC34A2	NM_001177998.2 linkuse as main transcript	c.549T>C	p.Ile183=	synonymous_variant	6/13		NP_001171469.2
SLC34A2	NM_001177999.2 linkuse as main transcript	c.549T>C	p.Ile183=	synonymous_variant	6/13		NP_001171470.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC34A2	ENST00000382051.8 linkuse as main transcript	c.552T>C	p.Ile184=	synonymous_variant	6/13	1	NM_006424.3	ENSP00000371483	P4	O95436-1

Frequencies

GnomAD3 genomes

AF:

0.0220

AC:

3346

AN:

152174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00666

Gnomad AMI

AF:

0.0329

Gnomad AMR

AF:

0.0256

Gnomad ASJ

AF:

0.0233

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00684

Gnomad FIN

AF:

0.0353

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0305

Gnomad OTH

AF:

0.0320

GnomAD3 exomes

AF:

0.0217

AC:

5446

AN:

251430

Hom.:

AF XY:

0.0220

AC XY:

2992

AN XY:

135888

show subpopulations

Gnomad AFR exome

AF:

0.00560

Gnomad AMR exome

AF:

0.0167

Gnomad ASJ exome

AF:

0.0195

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00817

Gnomad FIN exome

AF:

0.0335

Gnomad NFE exome

AF:

0.0302

Gnomad OTH exome

AF:

0.0272

GnomAD4 exome

AF:

0.0277

AC:

40464

AN:

1460526

Hom.:

710

Cov.:

AF XY:

0.0271

AC XY:

19677

AN XY:

726624

show subpopulations

Gnomad4 AFR exome

AF:

0.00574

Gnomad4 AMR exome

AF:

0.0169

Gnomad4 ASJ exome

AF:

0.0189

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00916

Gnomad4 FIN exome

AF:

0.0345

Gnomad4 NFE exome

AF:

0.0310

Gnomad4 OTH exome

AF:

0.0271

GnomAD4 genome

AF:

0.0220

AC:

3346

AN:

152292

Hom.:

Cov.:

AF XY:

0.0224

AC XY:

1666

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00667

Gnomad4 AMR

AF:

0.0255

Gnomad4 ASJ

AF:

0.0233

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00685

Gnomad4 FIN

AF:

0.0353

Gnomad4 NFE

AF:

0.0305

Gnomad4 OTH

AF:

0.0317

Alfa

AF:

0.0259

Hom.:

Bravo

AF:

0.0213

Asia WGS

AF:

0.00751

AC:

AN:

3478

EpiCase

AF:

0.0347

EpiControl

AF:

0.0341

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 21, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

4.5

DANN

Benign

0.76

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