rs17537076

Variant names:

• chr15-84921267-G-A
• rs17537076
• NM_004213.5:c.957+198G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC28A1	NM_004213.5	c.957+198G>A		intron_variant	Intron 11 of 18	ENST00000394573.6	NP_004204.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC28A1	ENST00000394573.6	c.957+198G>A		intron_variant	Intron 11 of 18	1	NM_004213.5	ENSP00000378074.1
SLC28A1	ENST00000286749.3	c.957+198G>A		intron_variant	Intron 10 of 17	1		ENSP00000286749.3
SLC28A1	ENST00000538177.5	c.957+198G>A		intron_variant	Intron 10 of 14	2		ENSP00000443752.1

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

African (AFR) AF: 0.0622 AC: 2580 AN: 41498

American (AMR) AF: 0.225 AC: 3438 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1356 AN: 3472

East Asian (EAS) AF: 0.0373 AC: 193 AN: 5174

South Asian (SAS) AF: 0.205 AC: 985 AN: 4814

European-Finnish (FIN) AF: 0.300 AC: 3175 AN: 10566

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.366 AC: 24895 AN: 67944

Other (OTH) AF: 0.295 AC: 620 AN: 2104

Alfa AF: 0.332 Hom.: 6974

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
PhyloP100		0.50
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: rs17537076; hg19: chr15-85464498;