rs12442557

chr15-84887913-G-A

Variant summary

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

The NM_004213.5(SLC28A1):c.96+57G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 1,289,002 control chromosomes in the GnomAD database, including 28,445 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 0.17 (2703 hom., cov: 32)
  • Exomes 𝑓: 0.21 (25742 hom.)
• Consequence: SLC28A1 NM_004213.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC28A1	NM_004213.5	c.96+57G>A		intron_variant		ENST00000394573.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC28A1	ENST00000394573.6	c.96+57G>A		intron_variant		1	NM_004213.5	P1
SLC28A1	ENST00000286749.3	c.96+57G>A		intron_variant		1		P1
SLC28A1	ENST00000338602.6	c.96+57G>A		intron_variant		1
SLC28A1	ENST00000538177.5	c.96+57G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25313 AN: 151974 Hom.: 2706 Cov.: 32

Gnomad AFR AF: 0.0398

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.183

GnomAD4 exome AF: 0.208 AC: 236763 AN: 1136910 Hom.: 25742 AF XY: 0.208 AC XY: 120923 AN XY: 581458

Gnomad4 AFR exome AF: 0.0336

Gnomad4 AMR exome AF: 0.199

Gnomad4 ASJ exome AF: 0.235

Gnomad4 EAS exome AF: 0.114

Gnomad4 SAS exome AF: 0.142

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.222

Gnomad4 OTH exome AF: 0.196

GnomAD4 genome AF: 0.166 AC: 25300 AN: 152092 Hom.: 2703 Cov.: 32 AF XY: 0.166 AC XY: 12358 AN XY: 74336

Gnomad4 AFR AF: 0.0398

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.181

Alfa AF: 0.217 Hom.: 6322

Bravo AF: 0.158

Asia WGS AF: 0.115 AC: 398 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	0.45
Dann	Benign	0.38

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: rs12442557; hg19: chr15-85431144; COSMIC: COSV54476333;