rs4697597

Variant names:

• chr4-25662622-G-A
• rs4697597
• NM_006424.3:c.112+10G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-25662622-G-A
• chr4-25662622-G-C
• chr4-25662622-G-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -3.17

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

Our verdict: Benign. The variant received -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	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC34A2	NM_006424.3	c.112+10G>A		intron_variant	Intron 2 of 12	ENST00000382051.8	NP_006415.3
SLC34A2	NM_001177998.2	c.112+10G>A		intron_variant	Intron 2 of 12		NP_001171469.2
SLC34A2	NM_001177999.2	c.112+10G>A		intron_variant	Intron 2 of 12		NP_001171470.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC34A2	ENST00000382051.8	c.112+10G>A		intron_variant	Intron 2 of 12	1	NM_006424.3	ENSP00000371483.3

Frequencies

GnomAD3 genomes AF: 0.0584 AC: 8879 AN: 151996 Hom.: 439 Cov.: 32

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

GnomAD2 exomes AF: 0.0745 AC: 18733 AN: 251482 AF XY: 0.0717

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 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.: 33 AF XY: 0.0464 AC XY: 33777 AN XY: 727198

African (AFR) AF: 0.0678 AC: 2271 AN: 33476

American (AMR) AF: 0.142 AC: 6361 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.0212 AC: 553 AN: 26136

East Asian (EAS) AF: 0.249 AC: 9901 AN: 39700

South Asian (SAS) AF: 0.0979 AC: 8447 AN: 86256

European-Finnish (FIN) AF: 0.0434 AC: 2321 AN: 53420

Middle Eastern (MID) AF: 0.0562 AC: 324 AN: 5768

European-Non Finnish (NFE) AF: 0.0297 AC: 33026 AN: 1111918

Other (OTH) AF: 0.0597 AC: 3607 AN: 60394

GnomAD4 genome AF: 0.0585 AC: 8901 AN: 152114 Hom.: 442 Cov.: 32 AF XY: 0.0626 AC XY: 4654 AN XY: 74348

African (AFR) AF: 0.0634 AC: 2630 AN: 41504

American (AMR) AF: 0.104 AC: 1596 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 91 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1363 AN: 5134

South Asian (SAS) AF: 0.105 AC: 506 AN: 4810

European-Finnish (FIN) AF: 0.0446 AC: 472 AN: 10594

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0300 AC: 2041 AN: 68004

Other (OTH) AF: 0.0654 AC: 138 AN: 2110

Alfa AF: 0.0234 Hom.: 16

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

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0030
DANN	Benign	0.65
PhyloP100		-3.2
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

Publications

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Other links and lift over

dbSNP: rs4697597; hg19: chr4-25664244; COSMIC: COSV65941723; COSMIC: COSV65941723;