rs7173860

chr15-84886310-A-Cchr15-84886310-A-T

Variant summary

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

The NM_004213.5(SLC28A1):c.-132-362A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 984,476 control chromosomes in the GnomAD database, including 83,613 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 0.43 (14005 hom., cov: 32)
  • Exomes 𝑓: 0.41 (69608 hom.)
• Consequence: SLC28A1 NM_004213.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

Genes affected

SLC28A1 (HGNC:11001): (solute carrier family 28 member 1) Enables azole transmembrane transporter activity; cytidine transmembrane transporter activity; and uridine transmembrane transporter activity. Involved in azole transmembrane transport; nucleoside transport; and pyrimidine-containing compound transmembrane transport. Located in cytosol; nuclear speck; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC28A1	NM_004213.5	c.-132-362A>C		intron_variant		ENST00000394573.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC28A1	ENST00000394573.6	c.-132-362A>C		intron_variant		1	NM_004213.5	P1
SLC28A1	ENST00000286749.3	c.-16-1435A>C		intron_variant		1		P1
SLC28A1	ENST00000338602.6	c.-132-362A>C		intron_variant		1
SLC28A1	ENST00000538177.5	c.-16-1435A>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64690 AN: 151760 Hom.: 14001 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.428

GnomAD4 exome AF: 0.409 AC: 340361 AN: 832600 Hom.: 69608 Cov.: 27 AF XY: 0.409 AC XY: 157251 AN XY: 384490

Gnomad4 AFR exome AF: 0.470

Gnomad4 AMR exome AF: 0.359

Gnomad4 ASJ exome AF: 0.485

Gnomad4 EAS exome AF: 0.496

Gnomad4 SAS exome AF: 0.337

Gnomad4 FIN exome AF: 0.442

Gnomad4 NFE exome AF: 0.408

Gnomad4 OTH exome AF: 0.416

GnomAD4 genome AF: 0.426 AC: 64726 AN: 151876 Hom.: 14005 Cov.: 32 AF XY: 0.424 AC XY: 31454 AN XY: 74220

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.425

Alfa AF: 0.415 Hom.: 18003

Bravo AF: 0.430

Asia WGS AF: 0.420 AC: 1459 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	1.0
Dann	Benign	0.49

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: rs7173860; hg19: chr15-85429541;