18-52338491-C-G

Position:

• chr18-52338491-C-G

Variant summary

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

The ENST00000582700.1(ENSG00000266335):​n.535G>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 0.632 in 152,124 control chromosomes in the GnomAD database, including 31,393 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 0.63 (31393 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENST00000582700.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000582700.1	n.535G>C		non_coding_transcript_exon_variant	1/2	3

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96034 AN: 152006 Hom.: 31346 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.631

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.632 AC: 96138 AN: 152124 Hom.: 31393 Cov.: 32 AF XY: 0.630 AC XY: 46876 AN XY: 74362

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.631

Alfa AF: 0.428 Hom.: 1050

Bravo AF: 0.652

Asia WGS AF: 0.676 AC: 2349 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	0.11
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs934345; hg19: chr18-49864861;