15-84921267-G-A

Position:

• chr15-84921267-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.957+198G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,038 control chromosomes in the GnomAD database, including 6,215 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 0.25 (6215 hom., cov: 31)
• Consequence: SLC28A1 NM_004213.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC28A1	NM_004213.5	c.957+198G>A		intron_variant		ENST00000394573.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC28A1	ENST00000394573.6	c.957+198G>A		intron_variant		1	NM_004213.5	P1
SLC28A1	ENST00000286749.3	c.957+198G>A		intron_variant		1		P1
SLC28A1	ENST00000538177.5	c.957+198G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37783 AN: 151920 Hom.: 6220 Cov.: 31

Gnomad AFR AF: 0.0623

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.0374

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.248 AC: 37764 AN: 152038 Hom.: 6215 Cov.: 31 AF XY: 0.242 AC XY: 18000 AN XY: 74330

Gnomad4 AFR AF: 0.0622

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.0373

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.295

Alfa AF: 0.333 Hom.: 5222

Bravo AF: 0.234

Asia WGS AF: 0.101 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.79

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: rs17537076; hg19: chr15-85464498;