chr4-99652026-C-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001354435.2(C4orf54):c.2623G>C(p.Glu875Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0123 in 1,536,122 control chromosomes in the GnomAD database, including 152 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0095 ( 12 hom., cov: 32)
Exomes 𝑓: 0.013 ( 140 hom. )
Consequence
C4orf54
NM_001354435.2 missense
NM_001354435.2 missense
Scores
1
2
12
Clinical Significance
Conservation
PhyloP100: 4.98
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.00588125).
BP6
Variant 4-99652026-C-G is Benign according to our data. Variant chr4-99652026-C-G is described in ClinVar as [Benign]. Clinvar id is 2654972.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 12 gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00950 AC: 1446AN: 152186Hom.: 11 Cov.: 32
GnomAD3 genomes
AF:
AC:
1446
AN:
152186
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0100 AC: 1347AN: 134578Hom.: 8 AF XY: 0.0107 AC XY: 783AN XY: 73302
GnomAD3 exomes
AF:
AC:
1347
AN:
134578
Hom.:
AF XY:
AC XY:
783
AN XY:
73302
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0126 AC: 17416AN: 1383818Hom.: 140 Cov.: 38 AF XY: 0.0124 AC XY: 8458AN XY: 682848
GnomAD4 exome
AF:
AC:
17416
AN:
1383818
Hom.:
Cov.:
38
AF XY:
AC XY:
8458
AN XY:
682848
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00953 AC: 1451AN: 152304Hom.: 12 Cov.: 32 AF XY: 0.00937 AC XY: 698AN XY: 74472
GnomAD4 genome
AF:
AC:
1451
AN:
152304
Hom.:
Cov.:
32
AF XY:
AC XY:
698
AN XY:
74472
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
46
ALSPAC
AF:
AC:
46
ExAC
AF:
AC:
116
Asia WGS
AF:
AC:
77
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Feb 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
C4orf54: BP4, BS1, BS2 -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Benign
T
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at