rs1051296

Variant names:

• chr21-45514947-A-C
• rs1051296
• NM_194255.4:c.*711T>G

Your query was ambiguous. Multiple possible variants found:

• chr21-45514947-A-C
• chr21-45514947-A-G
• chr21-45514947-A-T

Variant summary

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

The NM_194255.4(SLC19A1):​c.*711T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 1,448,090 control chromosomes in the GnomAD database, including 141,948 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 0.45 (15206 hom., cov: 33)
  • Exomes 𝑓: 0.44 (126742 hom.)
• Consequence: SLC19A1 NM_194255.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 38 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC19A1	NM_194255.4	c.*711T>G		3_prime_UTR_variant	Exon 6 of 6	ENST00000311124.9	NP_919231.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC19A1	ENST00000311124.9	c.*711T>G		3_prime_UTR_variant	Exon 6 of 6	1	NM_194255.4	ENSP00000308895.4

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67820 AN: 151842 Hom.: 15197 Cov.: 33

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.471

GnomAD2 exomes AF: 0.432 AC: 34746 AN: 80472 AF XY: 0.434

Gnomad AFR exome AF: 0.451

Gnomad AMR exome AF: 0.400

Gnomad ASJ exome AF: 0.387

Gnomad EAS exome AF: 0.544

Gnomad FIN exome AF: 0.430

Gnomad NFE exome AF: 0.418

Gnomad OTH exome AF: 0.441

GnomAD4 exome AF: 0.440 AC: 570280 AN: 1296128 Hom.: 126742 Cov.: 22 AF XY: 0.440 AC XY: 279957 AN XY: 635910

African (AFR) AF: 0.471 AC: 12305 AN: 26148

American (AMR) AF: 0.422 AC: 7560 AN: 17894

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 8488 AN: 21236

East Asian (EAS) AF: 0.580 AC: 18187 AN: 31366

South Asian (SAS) AF: 0.468 AC: 31184 AN: 66654

European-Finnish (FIN) AF: 0.439 AC: 20520 AN: 46704

Middle Eastern (MID) AF: 0.504 AC: 2621 AN: 5204

European-Non Finnish (NFE) AF: 0.434 AC: 445511 AN: 1027404

Other (OTH) AF: 0.447 AC: 23904 AN: 53518

GnomAD4 genome AF: 0.446 AC: 67846 AN: 151962 Hom.: 15206 Cov.: 33 AF XY: 0.449 AC XY: 33380 AN XY: 74282

African (AFR) AF: 0.464 AC: 19252 AN: 41454

American (AMR) AF: 0.429 AC: 6556 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1383 AN: 3472

East Asian (EAS) AF: 0.558 AC: 2853 AN: 5116

South Asian (SAS) AF: 0.481 AC: 2320 AN: 4822

European-Finnish (FIN) AF: 0.445 AC: 4714 AN: 10586

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29271 AN: 67924

Other (OTH) AF: 0.468 AC: 986 AN: 2108

Alfa AF: 0.440 Hom.: 19254

Bravo AF: 0.446

Asia WGS AF: 0.508 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.65
PhyloP100		-0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs1051296; hg19: chr21-46934861; COSMIC: COSV60589484; COSMIC: COSV60589484;