rs2413775

Variant names:

• chr15-45252090-T-A
• rs2413775
• ENST00000560344.6:n.1963A>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000560344.6(SLC28A2-AS1):​n.1963A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 424,826 control chromosomes in the GnomAD database, including 83,943 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 0.61 (29256 hom., cov: 33)
  • Exomes 𝑓: 0.62 (54687 hom.)
• Consequence: SLC28A2-AS1 ENST00000560344.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 9 publications found

Genes affected

SLC28A2-AS1 (HGNC:55417): (SLC28A2 antisense RNA 1)

SLC28A2 (HGNC:11002): (solute carrier family 28 member 2) Enables neurotransmitter transmembrane transporter activity and nucleoside transmembrane transporter activity. Involved in several processes, including nucleoside transport; purine nucleobase transmembrane transport; and pyrimidine-containing compound transmembrane transport. Predicted to be located in membrane. Predicted to be part of brush border membrane; coated vesicle; and vesicle membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560344.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A2-AS1	NR_120335.1		n.181-18A>T		intron	N/A
	SLC28A2	NM_004212.4	MANE Select	c.-205T>A		upstream_gene	N/A	NP_004203.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A2-AS1	ENST00000560344.6	TSL:5	n.1963A>T		non_coding_transcript_exon	Exon 4 of 4
	SLC28A2-AS1	ENST00000559003.5	TSL:2	n.244-18A>T		intron	N/A
	SLC28A2-AS1	ENST00000663463.1		n.56-9560A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92865 AN: 152058 Hom.: 29246 Cov.: 33

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.606

GnomAD4 exome AF: 0.621 AC: 169201 AN: 272650 Hom.: 54687 Cov.: 0 AF XY: 0.620 AC XY: 97245 AN XY: 156944

African (AFR) AF: 0.564 AC: 3588 AN: 6362

American (AMR) AF: 0.392 AC: 6552 AN: 16714

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 5815 AN: 9316

East Asian (EAS) AF: 0.195 AC: 1766 AN: 9062

South Asian (SAS) AF: 0.587 AC: 32098 AN: 54704

European-Finnish (FIN) AF: 0.633 AC: 7744 AN: 12226

Middle Eastern (MID) AF: 0.663 AC: 682 AN: 1028

European-Non Finnish (NFE) AF: 0.684 AC: 102952 AN: 150442

Other (OTH) AF: 0.626 AC: 8004 AN: 12796

GnomAD4 genome AF: 0.610 AC: 92897 AN: 152176 Hom.: 29256 Cov.: 33 AF XY: 0.605 AC XY: 45044 AN XY: 74408

African (AFR) AF: 0.577 AC: 23940 AN: 41516

American (AMR) AF: 0.502 AC: 7670 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2141 AN: 3472

East Asian (EAS) AF: 0.193 AC: 1001 AN: 5184

South Asian (SAS) AF: 0.570 AC: 2745 AN: 4814

European-Finnish (FIN) AF: 0.631 AC: 6673 AN: 10578

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46559 AN: 68006

Other (OTH) AF: 0.598 AC: 1264 AN: 2114

Alfa AF: 0.632 Hom.: 3832

Bravo AF: 0.596

Asia WGS AF: 0.395 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	16
DANN	Benign	0.78
PhyloP100		1.2
PromoterAI		-0.0025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2413775; hg19: chr15-45544288; COSMIC: COSV61665430;