15-45252121-T-G

Position:

• chr15-45252121-T-G

Variant summary

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

The NR_120335.1(SLC28A2-AS1):​n.181-49A>C variant causes a intron, non coding transcript 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 NR_120335.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC28A2-AS1	NR_120335.1	n.181-49A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC28A2-AS1	ENST00000663463.1	n.56-9591A>C		intron_variant, non_coding_transcript_variant
SLC28A2-AS1	ENST00000560344.6	n.1932A>C		non_coding_transcript_exon_variant	4/4	5
SLC28A2-AS1	ENST00000559003.5	n.244-49A>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR exome AF: 0.981

Gnomad4 AMR exome AF: 0.949

Gnomad4 ASJ exome AF: 0.981

Gnomad4 EAS exome AF: 0.795

Gnomad4 SAS exome AF: 0.991

Gnomad4 FIN exome AF: 0.998

Gnomad4 NFE exome AF: 0.997

Gnomad4 OTH exome AF: 0.980

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

Gnomad4 AFR AF: 0.985

Gnomad4 AMR AF: 0.968

Gnomad4 ASJ AF: 0.981

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.987

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.979

Alfa AF: 0.993 Hom.: 65506

Bravo AF: 0.980

Asia WGS AF: 0.893 AC: 3108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2899376; hg19: chr15-45544319;