chr18-43900562-C-T

Position:

• chr18-43900562-C-T

Variant summary

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

The variant allele was found at a frequency of 0.659 in 151,450 control chromosomes in the GnomAD database, including 33,072 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 0.66 (33072 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.43900562C>T		intergenic_region
LOC105372088	XR_935415.3	n.262+28511G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.659 AC: 99669 AN: 151334 Hom.: 33027 Cov.: 30

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.659 AC: 99775 AN: 151450 Hom.: 33072 Cov.: 30 AF XY: 0.661 AC XY: 48907 AN XY: 73992

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.841

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.643

Alfa AF: 0.634 Hom.: 61177

Bravo AF: 0.664

Asia WGS AF: 0.729 AC: 2533 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1380836; hg19: chr18-41480527;