chr20-32704020-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4BP6_ModerateBA1
The NM_053041.3(COMMD7):c.526+3G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00397 in 1,613,748 control chromosomes in the GnomAD database, including 223 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.022 ( 110 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 113 hom. )
Consequence
COMMD7
NM_053041.3 splice_donor_region, intron
NM_053041.3 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.004853
2
Clinical Significance
Conservation
PhyloP100: 2.36
Genes affected
COMMD7 (HGNC:16223): (COMM domain containing 7) Enables NF-kappaB binding activity. Involved in negative regulation of NF-kappaB transcription factor activity; negative regulation of transcription, DNA-templated; and tumor necrosis factor-mediated signaling pathway. Predicted to be located in cytoplasmic vesicle. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.15).
BP6
?
Variant 20-32704020-C-T is Benign according to our data. Variant chr20-32704020-C-T is described in ClinVar as [Benign]. Clinvar id is 777539.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0731 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COMMD7 | NM_053041.3 | c.526+3G>A | splice_donor_region_variant, intron_variant | ENST00000278980.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COMMD7 | ENST00000278980.11 | c.526+3G>A | splice_donor_region_variant, intron_variant | 1 | NM_053041.3 | P4 | |||
COMMD7 | ENST00000446419.6 | c.523+3G>A | splice_donor_region_variant, intron_variant | 2 | A1 | ||||
COMMD7 | ENST00000610160.1 | c.*442G>A | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0216 AC: 3280AN: 152150Hom.: 110 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
3280
AN:
152150
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: 0.00563 AC: 1401AN: 249056Hom.: 43 AF XY: 0.00423 AC XY: 571AN XY: 135112
GnomAD3 exomes
AF:
AC:
1401
AN:
249056
Hom.:
AF XY:
AC XY:
571
AN XY:
135112
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: 0.00213 AC: 3110AN: 1461480Hom.: 113 Cov.: 33 AF XY: 0.00179 AC XY: 1298AN XY: 727010
GnomAD4 exome
AF:
AC:
3110
AN:
1461480
Hom.:
Cov.:
33
AF XY:
AC XY:
1298
AN XY:
727010
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: 0.0216 AC: 3294AN: 152268Hom.: 110 Cov.: 32 AF XY: 0.0216 AC XY: 1605AN XY: 74462
GnomAD4 genome
?
AF:
AC:
3294
AN:
152268
Hom.:
Cov.:
32
AF XY:
AC XY:
1605
AN XY:
74462
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:
Asia WGS
AF:
AC:
19
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 26, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at