Variant rs3788200 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_194255.4(SLC19A1):c.189+1114T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 165,330 control chromosomes in the GnomAD database, including 24,154 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.54 ( 22279 hom., cov: 33)

Exomes 𝑓: 0.52 ( 1875 hom. )

Consequence

SLC19A1
NM_194255.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.31

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC19A1	NM_194255.4 link	c.189+1114T>C		intron_variant		ENST00000311124.9	NP_919231.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC19A1	ENST00000311124.9 link	c.189+1114T>C		intron_variant		1	NM_194255.4	ENSP00000308895.4		P41440-1

Frequencies

GnomAD3 genomes

AF:

0.538

AC:

81762

AN:

151938

Hom.:

22238

Cov.:

show subpopulations

Gnomad AFR

AF:

0.455

Gnomad AMI

AF:

0.689

Gnomad AMR

AF:

0.577

Gnomad ASJ

AF:

0.606

Gnomad EAS

AF:

0.473

Gnomad SAS

AF:

0.606

Gnomad FIN

AF:

0.549

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.573

Gnomad OTH

AF:

0.520

GnomAD4 exome

AF:

0.520

AC:

6899

AN:

13274

Hom.:

1875

AF XY:

0.522

AC XY:

3623

AN XY:

6944

show subpopulations

Gnomad4 AFR exome

AF:

0.360

Gnomad4 AMR exome

AF:

0.537

Gnomad4 ASJ exome

AF:

0.588

Gnomad4 EAS exome

AF:

0.417

Gnomad4 SAS exome

AF:

0.527

Gnomad4 FIN exome

AF:

0.519

Gnomad4 NFE exome

AF:

0.538

Gnomad4 OTH exome

AF:

0.557

GnomAD4 genome

AF:

0.538

AC:

81858

AN:

152056

Hom.:

22279

Cov.:

AF XY:

0.538

AC XY:

39998

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.456

Gnomad4 AMR

AF:

0.578

Gnomad4 ASJ

AF:

0.606

Gnomad4 EAS

AF:

0.472

Gnomad4 SAS

AF:

0.607

Gnomad4 FIN

AF:

0.549

Gnomad4 NFE

AF:

0.573

Gnomad4 OTH

AF:

0.526

Alfa

AF:

0.552

Hom.:

21277

Bravo

AF:

0.535

Asia WGS

AF:

0.551

AC:

1914

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.031

DANN

Benign

0.40

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over