rs2283135

Positions:

• chr10-117240421-C-G

Variant summary

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

The NR_184309.1(SLC18A2-AS1):​n.114-240G>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 0.079 in 151,882 control chromosomes in the GnomAD database, including 718 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 0.079 (718 hom., cov: 31)
• Consequence: SLC18A2-AS1 NR_184309.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

Genes affected

SLC18A2-AS1 (HGNC:55843): (SLC18A2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC18A2-AS1	NR_184309.1	n.114-240G>C		intron_variant, non_coding_transcript_variant
SLC18A2-AS1	NR_184310.1	n.237-240G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC18A2-AS1	ENST00000425264.2	n.238-240G>C		intron_variant, non_coding_transcript_variant		3
SLC18A2-AS1	ENST00000691914.2	n.114-240G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0790 AC: 11983 AN: 151762 Hom.: 715 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0279

Gnomad FIN AF: 0.0336

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0790 AC: 12006 AN: 151882 Hom.: 718 Cov.: 31 AF XY: 0.0804 AC XY: 5968 AN XY: 74216

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.0594

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.0281

Gnomad4 FIN AF: 0.0336

Gnomad4 NFE AF: 0.0415

Gnomad4 OTH AF: 0.0937

Alfa AF: 0.0637 Hom.: 55

Bravo AF: 0.0958

Asia WGS AF: 0.0900 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.1
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: rs2283135; hg19: chr10-118999932;