rs3788203

Variant names:

• chr21-45538672-T-G
• rs3788203
• NM_194255.4:c.-49-664A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_194255.4(SLC19A1):​c.-49-664A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,948 control chromosomes in the GnomAD database, including 22,096 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 (22096 hom., cov: 33)
• Consequence: SLC19A1 NM_194255.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 4 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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 rank	MANE	Protein	UniProt
SLC19A1	NM_194255.4	c.-49-664A>C		intron_variant	Intron 1 of 5	ENST00000311124.9	NP_919231.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC19A1	ENST00000311124.9	c.-49-664A>C		intron_variant	Intron 1 of 5	1	NM_194255.4	ENSP00000308895.4

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81411 AN: 151832 Hom.: 22057 Cov.: 33

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.519

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.536 AC: 81503 AN: 151948 Hom.: 22096 Cov.: 33 AF XY: 0.537 AC XY: 39875 AN XY: 74258

African (AFR) AF: 0.449 AC: 18597 AN: 41414

American (AMR) AF: 0.579 AC: 8848 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2097 AN: 3468

East Asian (EAS) AF: 0.474 AC: 2434 AN: 5140

South Asian (SAS) AF: 0.608 AC: 2932 AN: 4826

European-Finnish (FIN) AF: 0.550 AC: 5806 AN: 10552

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.573 AC: 38899 AN: 67942

Other (OTH) AF: 0.525 AC: 1110 AN: 2116

Alfa AF: 0.548 Hom.: 3012

Bravo AF: 0.532

Asia WGS AF: 0.550 AC: 1910 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.56
DANN	Benign	0.72
PhyloP100		-1.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.99
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3788203; hg19: chr21-46958586;