15-84972394-C-T

Variant names:

• chr15-84972394-C-T
• rs1109065
• NM_001321722.2:c.1875-3111C>T

Variant summary

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

The NM_001321722.2(SLC28A1):​c.1875-3111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,158 control chromosomes in the GnomAD database, including 30,514 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 0.63 (30514 hom., cov: 34)
• Consequence: SLC28A1 NM_001321722.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 0 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A1	NM_001321722.2	c.1875-3111C>T		intron_variant	Intron 18 of 18		NP_001308651.1
SLC28A1	NM_001321721.2	c.*43-3111C>T		intron_variant	Intron 16 of 16		NP_001308650.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95528 AN: 152040 Hom.: 30484 Cov.: 34

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.628 AC: 95603 AN: 152158 Hom.: 30514 Cov.: 34 AF XY: 0.633 AC XY: 47084 AN XY: 74394

African (AFR) AF: 0.559 AC: 23176 AN: 41494

American (AMR) AF: 0.679 AC: 10380 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2039 AN: 3472

East Asian (EAS) AF: 0.571 AC: 2961 AN: 5184

South Asian (SAS) AF: 0.802 AC: 3871 AN: 4824

European-Finnish (FIN) AF: 0.674 AC: 7136 AN: 10592

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44221 AN: 67992

Other (OTH) AF: 0.612 AC: 1293 AN: 2114

Alfa AF: 0.644 Hom.: 29870

Bravo AF: 0.621

Asia WGS AF: 0.672 AC: 2338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.26
PhyloP100		-0.025
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1109065; hg19: chr15-85515625;