rs2330183

chr21-45533378-C-Tchr21-45533378-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_194255.4(SLC19A1):c.190-1230G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,054 control chromosomes in the GnomAD database, including 20,711 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 0.51 (20711 hom., cov: 34)
• Consequence: SLC19A1 NM_194255.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC19A1	NM_194255.4	c.190-1230G>A		intron_variant		ENST00000311124.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC19A1	ENST00000311124.9	c.190-1230G>A		intron_variant		1	NM_194255.4	A2

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77450 AN: 151936 Hom.: 20686 Cov.: 34

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.510 AC: 77509 AN: 152054 Hom.: 20711 Cov.: 34 AF XY: 0.511 AC XY: 38001 AN XY: 74336

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.506

Alfa AF: 0.561 Hom.: 26471

Bravo AF: 0.502

Asia WGS AF: 0.529 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.6
Dann	Benign	0.48

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

Other links and lift over

dbSNP: rs2330183; hg19: chr21-46953292;