15-45252121-T-G

Variant names:

• chr15-45252121-T-G
• rs2899376
• ENST00000560344.6:n.1932A>C

Variant summary

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

The ENST00000560344.6(SLC28A2-AS1):​n.1932A>C 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 0.984 in 449,966 control chromosomes in the GnomAD database, including 218,045 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 0.98 (73733 hom., cov: 32)
  • Exomes 𝑓: 0.98 (144312 hom.)
• Consequence: SLC28A2-AS1 ENST00000560344.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 1 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 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.181-49A>C		intron	N/A
	SLC28A2	NM_004212.4	MANE Select	c.-174T>G		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.1932A>C		non_coding_transcript_exon	Exon 4 of 4
	SLC28A2-AS1	ENST00000559003.5	TSL:2	n.244-49A>C		intron	N/A
	SLC28A2-AS1	ENST00000663463.1		n.56-9591A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.983 AC: 149668 AN: 152226 Hom.: 73680 Cov.: 32

Gnomad AFR AF: 0.985

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.968

Gnomad ASJ AF: 0.981

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.982

GnomAD4 exome AF: 0.984 AC: 292841 AN: 297622 Hom.: 144312 Cov.: 0 AF XY: 0.985 AC XY: 167623 AN XY: 170152

African (AFR) AF: 0.981 AC: 8020 AN: 8172

American (AMR) AF: 0.949 AC: 24028 AN: 25314

Ashkenazi Jewish (ASJ) AF: 0.981 AC: 10385 AN: 10590

East Asian (EAS) AF: 0.795 AC: 7300 AN: 9188

South Asian (SAS) AF: 0.991 AC: 58690 AN: 59200

European-Finnish (FIN) AF: 0.998 AC: 12333 AN: 12354

Middle Eastern (MID) AF: 0.991 AC: 1098 AN: 1108

European-Non Finnish (NFE) AF: 0.997 AC: 157382 AN: 157818

Other (OTH) AF: 0.980 AC: 13605 AN: 13878

GnomAD4 genome AF: 0.983 AC: 149779 AN: 152344 Hom.: 73733 Cov.: 32 AF XY: 0.982 AC XY: 73158 AN XY: 74508

African (AFR) AF: 0.985 AC: 40948 AN: 41578

American (AMR) AF: 0.968 AC: 14807 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.981 AC: 3406 AN: 3472

East Asian (EAS) AF: 0.787 AC: 4074 AN: 5178

South Asian (SAS) AF: 0.987 AC: 4769 AN: 4830

European-Finnish (FIN) AF: 0.999 AC: 10614 AN: 10624

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67888 AN: 68042

Other (OTH) AF: 0.979 AC: 2072 AN: 2116

Alfa AF: 0.992 Hom.: 94606

Bravo AF: 0.980

Asia WGS AF: 0.893 AC: 3108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.1
DANN	Benign	0.72
PhyloP100		0.31
PromoterAI		0.059	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2899376; hg19: chr15-45544319;