ENST00000693093.3:n.380C>T

Variant names:

• chr21-45555934-C-T
• rs3827266
• ENST00000693093.3:n.380C>T

Variant summary

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

The ENST00000693093.3(ENSG00000288885):​n.380C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,014 control chromosomes in the GnomAD database, including 9,276 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 0.35 (9276 hom., cov: 33)
• Consequence: ENSG00000288885 ENST00000693093.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 9 publications found

Genes affected

ENSG00000288885 (HGNC:):

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=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC19A1	NM_001352511.3	c.-50+6808G>A		intron_variant	Intron 1 of 5		NP_001339440.1
SLC19A1	XM_011529696.3	c.-138+6808G>A		intron_variant	Intron 1 of 7		XP_011527998.1
SLC19A1	XM_047440954.1	c.-126+6808G>A		intron_variant	Intron 1 of 7		XP_047296910.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288885	ENST00000693093.3	n.380C>T		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000288885	ENST00000738773.1	n.32C>T		non_coding_transcript_exon_variant	Exon 1 of 2
SLC19A1	ENST00000650808.1	c.-50+6808G>A		intron_variant	Intron 1 of 5			ENSP00000498221.1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52527 AN: 151896 Hom.: 9265 Cov.: 33

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.346 AC: 52571 AN: 152014 Hom.: 9276 Cov.: 33 AF XY: 0.350 AC XY: 26000 AN XY: 74294

African (AFR) AF: 0.404 AC: 16758 AN: 41472

American (AMR) AF: 0.335 AC: 5131 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1000 AN: 3470

East Asian (EAS) AF: 0.454 AC: 2331 AN: 5140

South Asian (SAS) AF: 0.391 AC: 1884 AN: 4820

European-Finnish (FIN) AF: 0.361 AC: 3817 AN: 10574

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20569 AN: 67930

Other (OTH) AF: 0.312 AC: 658 AN: 2108

Alfa AF: 0.307 Hom.: 10160

Bravo AF: 0.344

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.5
DANN	Benign	0.88
PhyloP100		-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3827266; hg19: chr21-46975848;