Variant chr2-112647397-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_005415.5(SLC20A1):c.408A>C(p.Ala136=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00754 in 1,614,058 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0061 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0077 ( 66 hom. )

Consequence

SLC20A1
NM_005415.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.15

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 2-112647397-A-C is Benign according to our data. Variant chr2-112647397-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 2651282.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-112647397-A-C is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-1.15 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 66 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC20A1	NM_005415.5 linkuse as main transcript	c.408A>C	p.Ala136=	synonymous_variant	3/11	ENST00000272542.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC20A1	ENST00000272542.8 linkuse as main transcript	c.408A>C	p.Ala136=	synonymous_variant	3/11	1	NM_005415.5	P1
SLC20A1	ENST00000423633.5 linkuse as main transcript			upstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.00614

AC:

934

AN:

152104

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00140

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00478

Gnomad ASJ

AF:

0.0118

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00249

Gnomad FIN

AF:

0.00934

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00931

Gnomad OTH

AF:

0.00865

GnomAD3 exomes

AF:

0.00653

AC:

1641

AN:

251478

Hom.:

AF XY:

0.00696

AC XY:

946

AN XY:

135914

show subpopulations

Gnomad AFR exome

AF:

0.00123

Gnomad AMR exome

AF:

0.00315

Gnomad ASJ exome

AF:

0.00933

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00366

Gnomad FIN exome

AF:

0.00868

Gnomad NFE exome

AF:

0.00950

Gnomad OTH exome

AF:

0.00603

GnomAD4 exome

AF:

0.00769

AC:

11242

AN:

1461836

Hom.:

Cov.:

AF XY:

0.00770

AC XY:

5601

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.00137

Gnomad4 AMR exome

AF:

0.00322

Gnomad4 ASJ exome

AF:

0.00888

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00318

Gnomad4 FIN exome

AF:

0.00985

Gnomad4 NFE exome

AF:

0.00863

Gnomad4 OTH exome

AF:

0.00689

GnomAD4 genome

AF:

0.00614

AC:

934

AN:

152222

Hom.:

Cov.:

AF XY:

0.00568

AC XY:

423

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.00140

Gnomad4 AMR

AF:

0.00477

Gnomad4 ASJ

AF:

0.0118

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00249

Gnomad4 FIN

AF:

0.00934

Gnomad4 NFE

AF:

0.00931

Gnomad4 OTH

AF:

0.00856

Alfa

AF:

0.00758

Hom.:

Bravo

AF:

0.00549

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00911

EpiControl

AF:

0.00711

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

SLC20A1: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

8.4

DANN

Benign

0.64

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

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