Variant chr8-42417442-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001257180.2(SLC20A2):c.*361A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0696 in 165,108 control chromosomes in the GnomAD database, including 734 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.072 ( 708 hom., cov: 32)

Exomes 𝑓: 0.043 ( 26 hom. )

Consequence

SLC20A2
NM_001257180.2 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.29

Variant links:

Genes affected

SLC20A2 (HGNC:10947): (solute carrier family 20 member 2) This gene encodes a member of the inorganic phosphate transporter family. The encoded protein is a type 3 sodium-dependent phosphate symporter that plays an important role in phosphate homeostasis by mediating cellular phosphate uptake. The encoded protein also confers susceptibility to viral infection as a gamma-retroviral receptor. Mutations in this gene may play a role in familial idiopathic basal ganglia calcification. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Mar 2012]

SLC20A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP6

Variant 8-42417442-T-C is Benign according to our data. Variant chr8-42417442-T-C is described in ClinVar as [Benign]. Clinvar id is 363060.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC20A2	NM_001257180.2 linkuse as main transcript	c.*361A>G		3_prime_UTR_variant	11/11	ENST00000520262.6	NP_001244109.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC20A2	ENST00000520262.6 linkuse as main transcript	c.*361A>G		3_prime_UTR_variant	11/11	2	NM_001257180.2	ENSP00000429754	P1
SLC20A2	ENST00000342228.7 linkuse as main transcript	c.*361A>G		3_prime_UTR_variant	11/11	1		ENSP00000340465	P1

Frequencies

GnomAD3 genomes

AF:

0.0718

AC:

10918

AN:

152108

Hom.:

704

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.0312

Gnomad ASJ

AF:

0.0153

Gnomad EAS

AF:

0.0898

Gnomad SAS

AF:

0.0664

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0242

Gnomad OTH

AF:

0.0588

GnomAD4 exome

AF:

0.0428

AC:

551

AN:

12882

Hom.:

Cov.:

AF XY:

0.0452

AC XY:

304

AN XY:

6728

show subpopulations

Gnomad4 AFR exome

AF:

0.159

Gnomad4 AMR exome

AF:

0.0277

Gnomad4 ASJ exome

AF:

0.00508

Gnomad4 EAS exome

AF:

0.101

Gnomad4 SAS exome

AF:

0.0627

Gnomad4 FIN exome

AF:

0.0571

Gnomad4 NFE exome

AF:

0.0215

Gnomad4 OTH exome

AF:

0.0354

GnomAD4 genome

AF:

0.0719

AC:

10947

AN:

152226

Hom.:

708

Cov.:

AF XY:

0.0754

AC XY:

5613

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.161

Gnomad4 AMR

AF:

0.0312

Gnomad4 ASJ

AF:

0.0153

Gnomad4 EAS

AF:

0.0902

Gnomad4 SAS

AF:

0.0659

Gnomad4 FIN

AF:

0.106

Gnomad4 NFE

AF:

0.0242

Gnomad4 OTH

AF:

0.0615

Alfa

AF:

0.0296

Hom.:

224

Bravo

AF:

0.0704

Asia WGS

AF:

0.0950

AC:

330

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Idiopathic basal ganglia calcification 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Benign

0.88

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