21-45540981-C-T

Position:

• chr21-45540981-C-T

Variant summary

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

The NM_194255.4(SLC19A1):​c.-50+1387G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,956 control chromosomes in the GnomAD database, including 7,927 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 0.31 (7927 hom., cov: 32)
• Consequence: SLC19A1 NM_194255.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88

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 = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC19A1	NM_194255.4	c.-50+1387G>A		intron_variant		ENST00000311124.9	NP_919231.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC19A1	ENST00000311124.9	c.-50+1387G>A		intron_variant		1	NM_194255.4	ENSP00000308895.4

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46414 AN: 151838 Hom.: 7921 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.306 AC: 46448 AN: 151956 Hom.: 7927 Cov.: 32 AF XY: 0.314 AC XY: 23288 AN XY: 74266

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.320

Alfa AF: 0.320 Hom.: 1731

Bravo AF: 0.299

Asia WGS AF: 0.446 AC: 1555 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	4.0
DANN	Benign	0.74

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: rs13050920; hg19: chr21-46960895;