Variant 3-45755459-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_020208.4(SLC6A20):c.*3519G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,136 control chromosomes in the GnomAD database, including 11,036 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.35 ( 11031 hom., cov: 33)

Exomes 𝑓: 0.50 ( 5 hom. )

Consequence

SLC6A20
NM_020208.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.508

Variant links:

Genes affected

SLC6A20 (HGNC:30927): (solute carrier family 6 member 20) Transport of small hydrophilic substances across cell membranes is mediated by substrate-specific transporter proteins which have been classified into several families of related genes. The protein encoded by this gene belongs to the sodium:neurotransmitter symporter (SNF) family and functions as a proline transporter expressed in kidney and small intestine. Mutations in this gene are associated with Hyperglycinuria and Iminoglycinuria. [provided by RefSeq, Jul 2020]

SLC6A20 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 3-45755459-C-T is Benign according to our data. Variant chr3-45755459-C-T is described in ClinVar as [Benign]. Clinvar id is 345340.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A20	NM_020208.4 linkuse as main transcript	c.*3519G>A		3_prime_UTR_variant	11/11	ENST00000358525.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A20	ENST00000358525.9 linkuse as main transcript	c.*3519G>A		3_prime_UTR_variant	11/11	1	NM_020208.4	P1	Q9NP91-1
SLC6A20	ENST00000353278.8 linkuse as main transcript	c.*3519G>A		3_prime_UTR_variant	10/10	1			Q9NP91-2

Frequencies

GnomAD3 genomes

AF:

0.348

AC:

52957

AN:

151984

Hom.:

11032

Cov.:

show subpopulations

Gnomad AFR

AF:

0.130

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.342

Gnomad ASJ

AF:

0.506

Gnomad EAS

AF:

0.181

Gnomad SAS

AF:

0.272

Gnomad FIN

AF:

0.507

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.466

Gnomad OTH

AF:

0.377

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.500

GnomAD4 genome

AF:

0.348

AC:

52972

AN:

152102

Hom.:

11031

Cov.:

AF XY:

0.347

AC XY:

25827

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.130

Gnomad4 AMR

AF:

0.342

Gnomad4 ASJ

AF:

0.506

Gnomad4 EAS

AF:

0.181

Gnomad4 SAS

AF:

0.273

Gnomad4 FIN

AF:

0.507

Gnomad4 NFE

AF:

0.466

Gnomad4 OTH

AF:

0.373

Alfa

AF:

0.441

Hom.:

15879

Bravo

AF:

0.327

Asia WGS

AF:

0.215

AC:

751

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Hyperglycinuria

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

-0.74

CADD

Benign

2.5

DANN

Benign

0.79

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