chr1-45500031-G-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001102601.3(CCDC163):​c.-422C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 519,220 control chromosomes in the GnomAD database, including 135,946 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.74 ( 41787 hom., cov: 31)
Exomes 𝑓: 0.71 ( 94159 hom. )

Consequence

CCDC163
NM_001102601.3 5_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.682

Publications

20 publications found
Variant links:
Genes affected
CCDC163 (HGNC:27003): (CCDC163 homolog) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 1-45500031-G-T is Benign according to our data. Variant chr1-45500031-G-T is described in ClinVar as [Benign]. Clinvar id is 684370.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDC163NM_001102601.3 linkc.-422C>A 5_prime_UTR_variant Exon 1 of 5 ENST00000629482.3 NP_001096071.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCDC163ENST00000629482.3 linkc.-422C>A 5_prime_UTR_variant Exon 1 of 5 1 NM_001102601.3 ENSP00000486197.1 A0A0D9SF12

Frequencies

GnomAD3 genomes
AF:
0.738
AC:
112041
AN:
151912
Hom.:
41753
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.818
Gnomad AMI
AF:
0.762
Gnomad AMR
AF:
0.800
Gnomad ASJ
AF:
0.734
Gnomad EAS
AF:
0.942
Gnomad SAS
AF:
0.757
Gnomad FIN
AF:
0.678
Gnomad MID
AF:
0.756
Gnomad NFE
AF:
0.667
Gnomad OTH
AF:
0.735
GnomAD4 exome
AF:
0.711
AC:
260924
AN:
367190
Hom.:
94159
Cov.:
2
AF XY:
0.710
AC XY:
137491
AN XY:
193660
show subpopulations
African (AFR)
AF:
0.817
AC:
8828
AN:
10806
American (AMR)
AF:
0.844
AC:
13692
AN:
16228
Ashkenazi Jewish (ASJ)
AF:
0.731
AC:
8296
AN:
11348
East Asian (EAS)
AF:
0.950
AC:
22183
AN:
23342
South Asian (SAS)
AF:
0.733
AC:
31623
AN:
43162
European-Finnish (FIN)
AF:
0.675
AC:
14660
AN:
21720
Middle Eastern (MID)
AF:
0.757
AC:
1222
AN:
1614
European-Non Finnish (NFE)
AF:
0.667
AC:
145194
AN:
217706
Other (OTH)
AF:
0.716
AC:
15226
AN:
21264
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.510
Heterozygous variant carriers
0
3687
7374
11061
14748
18435
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
744
1488
2232
2976
3720
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.738
AC:
112131
AN:
152030
Hom.:
41787
Cov.:
31
AF XY:
0.742
AC XY:
55143
AN XY:
74310
show subpopulations
African (AFR)
AF:
0.818
AC:
33937
AN:
41496
American (AMR)
AF:
0.800
AC:
12224
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.734
AC:
2545
AN:
3468
East Asian (EAS)
AF:
0.942
AC:
4870
AN:
5170
South Asian (SAS)
AF:
0.757
AC:
3647
AN:
4818
European-Finnish (FIN)
AF:
0.678
AC:
7149
AN:
10544
Middle Eastern (MID)
AF:
0.762
AC:
224
AN:
294
European-Non Finnish (NFE)
AF:
0.667
AC:
45289
AN:
67944
Other (OTH)
AF:
0.737
AC:
1553
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1502
3005
4507
6010
7512
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
840
1680
2520
3360
4200
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.590
Hom.:
1749
Bravo
AF:
0.749
Asia WGS
AF:
0.857
AC:
2979
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided

- -

Jun 19, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
13
DANN
Benign
0.72
PhyloP100
0.68
PromoterAI
-0.052
Neutral
Mutation Taster
=100/0
polymorphism

Splicing

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

Publications

Other links and lift over

dbSNP: rs3748643; hg19: chr1-45965703; API