rs3775909

Variant names:

• chr4-25663707-C-G
• rs3775909
• NM_006424.3:c.251-495C>G

Your query was ambiguous. Multiple possible variants found:

• chr4-25663707-C-G
• chr4-25663707-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• pulmonary alveolar microlithiasis

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC34A2	NM_006424.3	c.251-495C>G		intron_variant	Intron 3 of 12	ENST00000382051.8	NP_006415.3
SLC34A2	NM_001177998.2	c.248-495C>G		intron_variant	Intron 3 of 12		NP_001171469.2
SLC34A2	NM_001177999.2	c.248-495C>G		intron_variant	Intron 3 of 12		NP_001171470.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC34A2	ENST00000382051.8	c.251-495C>G		intron_variant	Intron 3 of 12	1	NM_006424.3	ENSP00000371483.3

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

African (AFR) AF: 0.398 AC: 16524 AN: 41470

American (AMR) AF: 0.364 AC: 5560 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 803 AN: 3470

East Asian (EAS) AF: 0.592 AC: 3054 AN: 5156

South Asian (SAS) AF: 0.319 AC: 1533 AN: 4810

European-Finnish (FIN) AF: 0.161 AC: 1697 AN: 10566

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13699 AN: 67950

Other (OTH) AF: 0.313 AC: 662 AN: 2114

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
PhyloP100		-0.99
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3775909; hg19: chr4-25665329;