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GeneBe

rs4849091

chr2-112647131-G-Achr2-112647131-G-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_005415.5(SLC20A1):c.303G>A(p.Leu101=) 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 (★).

Frequency

Genomes: 𝑓 0.44 ( 16545 hom., cov: 31)
Exomes 𝑓: 0.54 ( 216710 hom. )

Consequence

SLC20A1
NM_005415.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter 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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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 criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.9 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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/exons MANE UniProt
SLC20A1NM_005415.5 linkuse as main transcriptc.303G>A p.Leu101= synonymous_variant 2/11 ENST00000272542.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC20A1ENST00000272542.8 linkuse as main transcriptc.303G>A p.Leu101= synonymous_variant 2/111 NM_005415.5 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.438
AC:
66562
AN:
151908
Hom.:
16541
Cov.:
31
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.:
53
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.438
AC:
66585
AN:
152026
Hom.:
16545
Cov.:
31
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: criteria provided, single submitter
LINK: link

Submissions by phenotype

SLC20A1-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesOct 17, 2019This 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.

Other links and lift over

dbSNP: rs4849091; hg19: chr2-113404708; COSMIC: COSV55611431; COSMIC: COSV55611431; API