18-22148845-C-A

Variant names:

• chr18-22148845-C-A
• rs62092220

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.179 in 152,076 control chromosomes in the GnomAD database, including 3,204 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (3204 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.166

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 18-22148845-C-A is Benign according to our data. Variant chr18-22148845-C-A is described in ClinVar as [Benign]. Clinvar id is 873213.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27188 AN: 151958 Hom.: 3202 Cov.: 32

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.179 AC: 27188 AN: 152076 Hom.: 3204 Cov.: 32 AF XY: 0.177 AC XY: 13142 AN XY: 74330

Gnomad4 AFR AF: 0.0505

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.161

Alfa AF: 0.142 Hom.: 390

Bravo AF: 0.163

Asia WGS AF: 0.0800 AC: 277 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Apr 02, 2020

Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: case-control

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62092220; hg19: chr18-19728806;