chr10-117240421-C-G

Variant names:

• chr10-117240421-C-G
• rs2283135
• ENST00000425264.3:n.272-240G>C

Variant summary

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

The ENST00000425264.3(SLC18A2-AS1):​n.272-240G>C variant causes a intron 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 ENST00000425264.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC18A2-AS1	NR_184309.1	n.114-240G>C		intron_variant	Intron 1 of 1
SLC18A2-AS1	NR_184310.1	n.237-240G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC18A2-AS1	ENST00000425264.3	n.272-240G>C		intron_variant	Intron 2 of 2	3
SLC18A2-AS1	ENST00000691914.3	n.149-240G>C		intron_variant	Intron 1 of 1
SLC18A2-AS1	ENST00000758985.1	n.244-240G>C		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.123 AC: 5104 AN: 41402

American (AMR) AF: 0.164 AC: 2503 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0594 AC: 206 AN: 3468

East Asian (EAS) AF: 0.124 AC: 631 AN: 5102

South Asian (SAS) AF: 0.0281 AC: 135 AN: 4802

European-Finnish (FIN) AF: 0.0336 AC: 356 AN: 10602

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0415 AC: 2820 AN: 67934

Other (OTH) AF: 0.0937 AC: 197 AN: 2102

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
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs2283135; hg19: chr10-118999932;