chr18-22636284-T-C

Position:

• chr18-22636284-T-C

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 0.83 in 152,134 control chromosomes in the GnomAD database, including 52,717 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 0.83 (52717 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.848 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

Frequencies

GnomAD3 genomes AF: 0.830 AC: 126247 AN: 152016 Hom.: 52677 Cov.: 32

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.830 AC: 126340 AN: 152134 Hom.: 52717 Cov.: 32 AF XY: 0.829 AC XY: 61656 AN XY: 74366

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.898

Gnomad4 NFE AF: 0.854

Gnomad4 OTH AF: 0.835

Alfa AF: 0.842 Hom.: 9125

Bravo AF: 0.826

Asia WGS AF: 0.661 AC: 2299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11876485; hg19: chr18-20216247;