18-22148845-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.166
Variant links:

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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
show subpopulations
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
show subpopulations
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
LINK: link

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs62092220; hg19: chr18-19728806; API