dbSNP rs1051298: SLC19A1:c.*746C>T (chr21-45514912-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_194255.4(SLC19A1):c.*746C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 1,285,862 control chromosomes in the GnomAD database, including 130,437 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 0.46 ( 16600 hom., cov: 33)

Exomes 𝑓: 0.45 ( 113837 hom. )

Consequence

SLC19A1
NM_194255.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.71

Publications

37 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC19A1	NM_194255.4 link	c.*746C>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000311124.9	NP_919231.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC19A1	ENST00000311124.9 link	c.*746C>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_194255.4	ENSP00000308895.4		P41440-1

Frequencies

GnomAD3 genomes

AF:

0.465

AC:

70592

AN:

151890

Hom.:

16589

Cov.:

show subpopulations

Gnomad AFR

AF:

0.522

Gnomad AMI

AF:

0.408

Gnomad AMR

AF:

0.437

Gnomad ASJ

AF:

0.398

Gnomad EAS

AF:

0.552

Gnomad SAS

AF:

0.522

Gnomad FIN

AF:

0.446

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.432

Gnomad OTH

AF:

0.485

GnomAD4 exome

AF:

0.446

AC:

506192

AN:

1133850

Hom.:

113837

Cov.:

AF XY:

0.447

AC XY:

248916

AN XY:

556756

show subpopulations

African (AFR)

AF:

0.535

AC:

12263

AN:

22932

American (AMR)

AF:

0.431

AC:

6318

AN:

14666

Ashkenazi Jewish (ASJ)

AF:

0.401

AC:

7270

AN:

18112

East Asian (EAS)

AF:

0.577

AC:

17164

AN:

29754

South Asian (SAS)

AF:

0.506

AC:

28154

AN:

55620

European-Finnish (FIN)

AF:

0.438

AC:

19390

AN:

44228

Middle Eastern (MID)

AF:

0.521

AC:

2172

AN:

4168

European-Non Finnish (NFE)

AF:

0.437

AC:

391661

AN:

896632

Other (OTH)

AF:

0.457

AC:

21800

AN:

47738

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

13541

27083

40624

54166

67707

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11944

23888

35832

47776

59720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.465

AC:

70628

AN:

152012

Hom.:

16600

Cov.:

AF XY:

0.467

AC XY:

34717

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.522

AC:

21648

AN:

41468

American (AMR)

AF:

0.436

AC:

6673

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.398

AC:

1381

AN:

3468

East Asian (EAS)

AF:

0.553

AC:

2830

AN:

5120

South Asian (SAS)

AF:

0.522

AC:

2518

AN:

4822

European-Finnish (FIN)

AF:

0.446

AC:

4709

AN:

10570

Middle Eastern (MID)

AF:

0.500

AC:

147

AN:

294

European-Non Finnish (NFE)

AF:

0.432

AC:

29335

AN:

67958

Other (OTH)

AF:

0.482

AC:

1016

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1981

3962

5944

7925

9906

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

650

1300

1950

2600

3250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.445

Hom.:

15976

Bravo

AF:

0.466

Asia WGS

AF:

0.532

AC:

1850

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.55

(source)

DANN

Benign

0.55

PhyloP100

-1.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over