dbSNP rs4849091: SLC20A1:p.Leu101Leu (chr2-112647131-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_005415.5(SLC20A1):c.303G>A(p.Leu101Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 1,613,440 control chromosomes in the GnomAD database, including 233,255 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.44 ( 16545 hom., cov: 31)

Exomes 𝑓: 0.54 ( 216710 hom. )

Consequence

SLC20A1
NM_005415.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.900

Variant links:

Genes affected

SLC20A1 (HGNC:10946): (solute carrier family 20 member 1) The protein encoded by this gene is a sodium-phosphate symporter that absorbs phosphate from interstitial fluid for use in cellular functions such as metabolism, signal transduction, and nucleic acid and lipid synthesis. The encoded protein is also a retroviral receptor, causing human cells to be susceptible to infection by gibbon ape leukemia virus, simian sarcoma-associated virus, feline leukemia virus subgroup B, and 10A1 murine leukemia virus.[provided by RefSeq, Mar 2011]

SLC20A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 2-112647131-G-A is Benign according to our data. Variant chr2-112647131-G-A is described in ClinVar as [Benign]. Clinvar id is 3058938.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.9 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC20A1	NM_005415.5 link	c.303G>A	p.Leu101Leu	synonymous_variant	Exon 2 of 11	ENST00000272542.8	NP_005406.3	Q8WUM9A7LNJ1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC20A1	ENST00000272542.8 link	c.303G>A	p.Leu101Leu	synonymous_variant	Exon 2 of 11	1	NM_005415.5	ENSP00000272542.3		Q8WUM9

Frequencies

GnomAD3 genomes

AF:

0.438

AC:

66562

AN:

151908

Hom.:

16541

Cov.:

show subpopulations

Gnomad AFR

AF:

0.204

Gnomad AMI

AF:

0.525

Gnomad AMR

AF:

0.467

Gnomad ASJ

AF:

0.530

Gnomad EAS

AF:

0.209

Gnomad SAS

AF:

0.484

Gnomad FIN

AF:

0.565

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.561

Gnomad OTH

AF:

0.467

GnomAD3 exomes

AF:

0.493

AC:

123453

AN:

250338

Hom.:

32341

AF XY:

0.503

AC XY:

68105

AN XY:

135440

show subpopulations

Gnomad AFR exome

AF:

0.197

Gnomad AMR exome

AF:

0.480

Gnomad ASJ exome

AF:

0.537

Gnomad EAS exome

AF:

0.213

Gnomad SAS exome

AF:

0.489

Gnomad FIN exome

AF:

0.569

Gnomad NFE exome

AF:

0.566

Gnomad OTH exome

AF:

0.536

GnomAD4 exome

AF:

0.537

AC:

785014

AN:

1461414

Hom.:

216710

Cov.:

AF XY:

0.538

AC XY:

390905

AN XY:

726958

show subpopulations

Gnomad4 AFR exome

AF:

0.192

Gnomad4 AMR exome

AF:

0.481

Gnomad4 ASJ exome

AF:

0.540

Gnomad4 EAS exome

AF:

0.199

Gnomad4 SAS exome

AF:

0.491

Gnomad4 FIN exome

AF:

0.569

Gnomad4 NFE exome

AF:

0.565

Gnomad4 OTH exome

AF:

0.517

GnomAD4 genome

AF:

0.438

AC:

66585

AN:

152026

Hom.:

16545

Cov.:

AF XY:

0.438

AC XY:

32546

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.204

Gnomad4 AMR

AF:

0.467

Gnomad4 ASJ

AF:

0.530

Gnomad4 EAS

AF:

0.208

Gnomad4 SAS

AF:

0.484

Gnomad4 FIN

AF:

0.565

Gnomad4 NFE

AF:

0.561

Gnomad4 OTH

AF:

0.470

Alfa

AF:

0.535

Hom.:

40542

Bravo

AF:

0.425

Asia WGS

AF:

0.362

AC:

1259

AN:

3478

EpiCase

AF:

0.564

EpiControl

AF:

0.568

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SLC20A1-related disorder

Benign:1

Oct 17, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

7.6

DANN

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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