Variant 21-45538002-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_194255.4(SLC19A1):c.-43C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 1,437,318 control chromosomes in the GnomAD database, including 221,635 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.50 ( 20155 hom., cov: 32)

Exomes 𝑓: 0.56 ( 201480 hom. )

Consequence

SLC19A1
NM_194255.4 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.13

Variant links:

Genes affected

SLC19A1 (HGNC:10937): (solute carrier family 19 member 1) The membrane protein encoded by this gene is a transporter of folate and is involved in the regulation of intracellular concentrations of folate. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2011]

SLC19A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 21-45538002-G-A is Benign according to our data. Variant chr21-45538002-G-A is described in ClinVar as [Benign]. Clinvar id is 1220816.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC19A1	NM_194255.4 linkuse as main transcript	c.-43C>T		5_prime_UTR_variant	2/6	ENST00000311124.9	NP_919231.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC19A1	ENST00000311124.9 linkuse as main transcript	c.-43C>T		5_prime_UTR_variant	2/6	1	NM_194255.4	ENSP00000308895	A2	P41440-1

Frequencies

GnomAD3 genomes

AF:

0.504

AC:

76469

AN:

151792

Hom.:

20135

Cov.:

show subpopulations

Gnomad AFR

AF:

0.341

Gnomad AMI

AF:

0.686

Gnomad AMR

AF:

0.563

Gnomad ASJ

AF:

0.601

Gnomad EAS

AF:

0.471

Gnomad SAS

AF:

0.593

Gnomad FIN

AF:

0.548

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.571

Gnomad OTH

AF:

0.494

GnomAD3 exomes

AF:

0.522

AC:

47113

AN:

90294

Hom.:

12320

AF XY:

0.528

AC XY:

24752

AN XY:

46874

show subpopulations

Gnomad AFR exome

AF:

0.318

Gnomad AMR exome

AF:

0.549

Gnomad ASJ exome

AF:

0.577

Gnomad EAS exome

AF:

0.442

Gnomad SAS exome

AF:

0.568

Gnomad FIN exome

AF:

0.524

Gnomad NFE exome

AF:

0.548

Gnomad OTH exome

AF:

0.523

GnomAD4 exome

AF:

0.557

AC:

716515

AN:

1285408

Hom.:

201480

Cov.:

AF XY:

0.559

AC XY:

349314

AN XY:

625410

show subpopulations

Gnomad4 AFR exome

AF:

0.320

Gnomad4 AMR exome

AF:

0.552

Gnomad4 ASJ exome

AF:

0.588

Gnomad4 EAS exome

AF:

0.444

Gnomad4 SAS exome

AF:

0.584

Gnomad4 FIN exome

AF:

0.546

Gnomad4 NFE exome

AF:

0.567

Gnomad4 OTH exome

AF:

0.545

GnomAD4 genome

AF:

0.504

AC:

76519

AN:

151910

Hom.:

20155

Cov.:

AF XY:

0.505

AC XY:

37521

AN XY:

74230

show subpopulations

Gnomad4 AFR

AF:

0.341

Gnomad4 AMR

AF:

0.564

Gnomad4 ASJ

AF:

0.601

Gnomad4 EAS

AF:

0.471

Gnomad4 SAS

AF:

0.594

Gnomad4 FIN

AF:

0.548

Gnomad4 NFE

AF:

0.571

Gnomad4 OTH

AF:

0.500

Alfa

AF:

0.559

Hom.:

12741

Bravo

AF:

0.497

Asia WGS

AF:

0.531

AC:

1844

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 24, 2019	This variant is associated with the following publications: (PMID: 17404734, 18053808) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.4

DANN

Benign

0.53

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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