chr15-84913115-T-G

Position:

• chr15-84913115-T-G

Variant summary

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

The NM_004213.5(SLC28A1):​c.795+4320T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,020 control chromosomes in the GnomAD database, including 36,461 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 0.69 (36461 hom., cov: 31)
• Consequence: SLC28A1 NM_004213.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

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]

(HGNC:):

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 = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC28A1	NM_004213.5	c.795+4320T>G		intron_variant		ENST00000394573.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC28A1	ENST00000394573.6	c.795+4320T>G		intron_variant		1	NM_004213.5	P1
SLC28A1	ENST00000286749.3	c.795+4320T>G		intron_variant		1		P1
SLC28A1	ENST00000538177.5	c.795+4320T>G		intron_variant		2
	ENST00000657848.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104941 AN: 151902 Hom.: 36412 Cov.: 31

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.691 AC: 105050 AN: 152020 Hom.: 36461 Cov.: 31 AF XY: 0.690 AC XY: 51274 AN XY: 74304

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.698

Alfa AF: 0.681 Hom.: 44666

Bravo AF: 0.697

Asia WGS AF: 0.860 AC: 2990 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	3.0
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: rs11853372; hg19: chr15-85456346;