chr5-116240442-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016144.4(COMMD10):​c.511-51075A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,182 control chromosomes in the GnomAD database, including 1,322 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 0.11 ( 1322 hom., cov: 32)

Consequence

COMMD10
NM_016144.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60

Publications

3 publications found
Variant links:
Genes affected
COMMD10 (HGNC:30201): (COMM domain containing 10) Located in nucleoplasm. [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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COMMD10NM_016144.4 linkc.511-51075A>G intron_variant Intron 5 of 6 ENST00000274458.9 NP_057228.1 Q9Y6G5
COMMD10NM_001308080.2 linkc.469-51075A>G intron_variant Intron 5 of 6 NP_001295009.1 Q9Y6G5D6RJ90

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COMMD10ENST00000274458.9 linkc.511-51075A>G intron_variant Intron 5 of 6 1 NM_016144.4 ENSP00000274458.4 Q9Y6G5

Frequencies

GnomAD3 genomes
AF:
0.109
AC:
16507
AN:
152064
Hom.:
1324
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.220
Gnomad AMI
AF:
0.0461
Gnomad AMR
AF:
0.0720
Gnomad ASJ
AF:
0.116
Gnomad EAS
AF:
0.176
Gnomad SAS
AF:
0.0560
Gnomad FIN
AF:
0.0585
Gnomad MID
AF:
0.0854
Gnomad NFE
AF:
0.0556
Gnomad OTH
AF:
0.111
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.108
AC:
16508
AN:
152182
Hom.:
1322
Cov.:
32
AF XY:
0.108
AC XY:
8044
AN XY:
74398
show subpopulations
African (AFR)
AF:
0.220
AC:
9122
AN:
41478
American (AMR)
AF:
0.0717
AC:
1096
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.116
AC:
402
AN:
3470
East Asian (EAS)
AF:
0.176
AC:
913
AN:
5174
South Asian (SAS)
AF:
0.0558
AC:
269
AN:
4820
European-Finnish (FIN)
AF:
0.0585
AC:
621
AN:
10614
Middle Eastern (MID)
AF:
0.0884
AC:
26
AN:
294
European-Non Finnish (NFE)
AF:
0.0556
AC:
3784
AN:
68014
Other (OTH)
AF:
0.110
AC:
233
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
712
1424
2137
2849
3561
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
176
352
528
704
880
<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:
0.0381
Hom.:
59
Bravo
AF:
0.118
Asia WGS
AF:
0.120
AC:
416
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
5.2
DANN
Benign
0.77
PhyloP100
1.6
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs17139253; hg19: chr5-115576139; API