Variant chr4-25662622-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_006424.3(SLC34A2):c.112+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0469 in 1,613,906 control chromosomes in the GnomAD database, including 3,681 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.059 ( 442 hom., cov: 32)

Exomes 𝑓: 0.046 ( 3239 hom. )

Consequence

SLC34A2
NM_006424.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.17

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:

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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=-0.94).

BP6

Variant 4-25662622-G-A is Benign according to our data. Variant chr4-25662622-G-A is described in ClinVar as [Benign]. Clinvar id is 1600581.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-25662622-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
SLC34A2	NM_006424.3 linkuse as main transcript	c.112+10G>A	intron_variant	ENST00000382051.8	NP_006415.3
SLC34A2	NM_001177998.2 linkuse as main transcript	c.112+10G>A	intron_variant		NP_001171469.2
SLC34A2	NM_001177999.2 linkuse as main transcript	c.112+10G>A	intron_variant		NP_001171470.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC34A2	ENST00000382051.8 linkuse as main transcript	c.112+10G>A		intron_variant		1	NM_006424.3	ENSP00000371483	P4	O95436-1

Frequencies

GnomAD3 genomes

AF:

0.0584

AC:

8879

AN:

151996

Hom.:

439

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0632

Gnomad AMI

AF:

0.0471

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.0262

Gnomad EAS

AF:

0.265

Gnomad SAS

AF:

0.106

Gnomad FIN

AF:

0.0446

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0300

Gnomad OTH

AF:

0.0642

GnomAD3 exomes

AF:

0.0745

AC:

18733

AN:

251482

Hom.:

1304

AF XY:

0.0717

AC XY:

9748

AN XY:

135916

show subpopulations

Gnomad AFR exome

AF:

0.0672

Gnomad AMR exome

AF:

0.146

Gnomad ASJ exome

AF:

0.0222

Gnomad EAS exome

AF:

0.258

Gnomad SAS exome

AF:

0.0958

Gnomad FIN exome

AF:

0.0421

Gnomad NFE exome

AF:

0.0297

Gnomad OTH exome

AF:

0.0645

GnomAD4 exome

AF:

0.0457

AC:

66811

AN:

1461792

Hom.:

3239

Cov.:

AF XY:

0.0464

AC XY:

33777

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.0678

Gnomad4 AMR exome

AF:

0.142

Gnomad4 ASJ exome

AF:

0.0212

Gnomad4 EAS exome

AF:

0.249

Gnomad4 SAS exome

AF:

0.0979

Gnomad4 FIN exome

AF:

0.0434

Gnomad4 NFE exome

AF:

0.0297

Gnomad4 OTH exome

AF:

0.0597

GnomAD4 genome

AF:

0.0585

AC:

8901

AN:

152114

Hom.:

442

Cov.:

AF XY:

0.0626

AC XY:

4654

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.0634

Gnomad4 AMR

AF:

0.104

Gnomad4 ASJ

AF:

0.0262

Gnomad4 EAS

AF:

0.265

Gnomad4 SAS

AF:

0.105

Gnomad4 FIN

AF:

0.0446

Gnomad4 NFE

AF:

0.0300

Gnomad4 OTH

AF:

0.0654

Alfa

AF:

0.0224

Hom.:

Bravo

AF:

0.0646

Asia WGS

AF:

0.203

AC:

705

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 23, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.0030

DANN

Benign

0.65

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