rs3775909

chr4-25663707-C-Gchr4-25663707-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006424.3(SLC34A2):c.251-495C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,034 control chromosomes in the GnomAD database, including 7,349 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (7349 hom., cov: 32)
• Consequence: SLC34A2 NM_006424.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC34A2	NM_006424.3	c.251-495C>G		intron_variant		ENST00000382051.8
SLC34A2	NM_001177998.2	c.248-495C>G		intron_variant
SLC34A2	NM_001177999.2	c.248-495C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC34A2	ENST00000382051.8	c.251-495C>G		intron_variant		1	NM_006424.3	P4

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43688 AN: 151914 Hom.: 7338 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.313

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.288 AC: 43735 AN: 152034 Hom.: 7349 Cov.: 32 AF XY: 0.292 AC XY: 21712 AN XY: 74312

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.313

Alfa AF: 0.0988 Hom.: 140

Bravo AF: 0.307

Asia WGS AF: 0.466 AC: 1619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.82
Dann	Benign	0.41

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

Other links and lift over

dbSNP: rs3775909; hg19: chr4-25665329;