18-12280923-A-G

Position:

• chr18-12280923-A-G

Variant summary

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

The ENST00000623093.1(ENSG00000280302):​n.1497A>G 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 0.353 in 152,124 control chromosomes in the GnomAD database, including 9,632 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 0.35 (9628 hom., cov: 32)
  • Exomes 𝑓: 0.35 (4 hom.)
• Consequence: ENSG00000280302 ENST00000623093.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.87

Genes affected

ENSG00000280302 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.12280923A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000280302	ENST00000623093.1	n.1497A>G		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53671 AN: 151932 Hom.: 9616 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.369

GnomAD4 exome AF: 0.351 AC: 26 AN: 74 Hom.: 4 Cov.: 0 AF XY: 0.353 AC XY: 24 AN XY: 68

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.353

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.353 AC: 53714 AN: 152050 Hom.: 9628 Cov.: 32 AF XY: 0.357 AC XY: 26513 AN XY: 74346

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.371

Alfa AF: 0.372 Hom.: 5420

Bravo AF: 0.345

Asia WGS AF: 0.376 AC: 1308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6505744; hg19: chr18-12280922;