rs914232

Positions:

• chr21-45532836-T-C

Variant summary

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

The NM_194255.4(SLC19A1):​c.190-688A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 152,110 control chromosomes in the GnomAD database, including 21,941 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 0.53 (21941 hom., cov: 34)
• Consequence: SLC19A1 NM_194255.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC19A1	NM_194255.4	c.190-688A>G		intron_variant		ENST00000311124.9	NP_919231.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC19A1	ENST00000311124.9	c.190-688A>G		intron_variant		1	NM_194255.4	ENSP00000308895	A2

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80750 AN: 151992 Hom.: 21912 Cov.: 34

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.531 AC: 80826 AN: 152110 Hom.: 21941 Cov.: 34 AF XY: 0.532 AC XY: 39563 AN XY: 74360

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.524

Alfa AF: 0.572 Hom.: 32116

Bravo AF: 0.526

Asia WGS AF: 0.544 AC: 1890 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.53
DANN	Benign	0.41

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: rs914232; hg19: chr21-46952750;