chr7-123502681-T-C
Position:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_178827.5(IQUB):āc.939A>Gā(p.Val313=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00266 in 1,610,678 control chromosomes in the GnomAD database, including 109 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.014 ( 53 hom., cov: 32)
Exomes š: 0.0014 ( 56 hom. )
Consequence
IQUB
NM_178827.5 synonymous
NM_178827.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.402
Genes affected
IQUB (HGNC:21995): (IQ motif and ubiquitin domain containing) Predicted to be involved in cilium assembly. Predicted to act upstream of or within smoothened signaling pathway. Predicted to be active in acrosomal vesicle and motile cilium. [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 -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 7-123502681-T-C is Benign according to our data. Variant chr7-123502681-T-C is described in ClinVar as [Benign]. Clinvar id is 778333.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.402 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0144 (2191/152328) while in subpopulation AFR AF= 0.0495 (2060/41576). AF 95% confidence interval is 0.0478. There are 53 homozygotes in gnomad4. There are 1040 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 53 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQUB | NM_178827.5 | c.939A>G | p.Val313= | synonymous_variant | 6/13 | ENST00000324698.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQUB | ENST00000324698.11 | c.939A>G | p.Val313= | synonymous_variant | 6/13 | 1 | NM_178827.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0144 AC: 2187AN: 152210Hom.: 53 Cov.: 32
GnomAD3 genomes
AF:
AC:
2187
AN:
152210
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: 0.00353 AC: 881AN: 249758Hom.: 27 AF XY: 0.00282 AC XY: 380AN XY: 134968
GnomAD3 exomes
AF:
AC:
881
AN:
249758
Hom.:
AF XY:
AC XY:
380
AN XY:
134968
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: 0.00143 AC: 2091AN: 1458350Hom.: 56 Cov.: 30 AF XY: 0.00128 AC XY: 930AN XY: 725546
GnomAD4 exome
AF:
AC:
2091
AN:
1458350
Hom.:
Cov.:
30
AF XY:
AC XY:
930
AN XY:
725546
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: 0.0144 AC: 2191AN: 152328Hom.: 53 Cov.: 32 AF XY: 0.0140 AC XY: 1040AN XY: 74500
GnomAD4 genome
AF:
AC:
2191
AN:
152328
Hom.:
Cov.:
32
AF XY:
AC XY:
1040
AN XY:
74500
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:
10
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 | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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