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GeneBe

7-123502681-T-C

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_178827.5(IQUB):c.939A>G(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 (★).

Frequency

Genomes: 𝑓 0.014 ( 53 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 56 hom. )

Consequence

IQUB
NM_178827.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.402
Variant links:
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
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.402 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
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
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 53 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IQUBNM_178827.5 linkuse as main transcriptc.939A>G p.Val313= synonymous_variant 6/13 ENST00000324698.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IQUBENST00000324698.11 linkuse as main transcriptc.939A>G p.Val313= synonymous_variant 6/131 NM_178827.5 P1Q8NA54-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0144
AC:
2187
AN:
152210
Hom.:
53
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0496
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00596
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000235
Gnomad OTH
AF:
0.0100
GnomAD3 exomes
AF:
0.00353
AC:
881
AN:
249758
Hom.:
27
AF XY:
0.00282
AC XY:
380
AN XY:
134968
show subpopulations
Gnomad AFR exome
AF:
0.0474
Gnomad AMR exome
AF:
0.00210
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000331
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000230
Gnomad OTH exome
AF:
0.00230
GnomAD4 exome
AF:
0.00143
AC:
2091
AN:
1458350
Hom.:
56
Cov.:
30
AF XY:
0.00128
AC XY:
930
AN XY:
725546
show subpopulations
Gnomad4 AFR exome
AF:
0.0490
Gnomad4 AMR exome
AF:
0.00247
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000140
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000116
Gnomad4 OTH exome
AF:
0.00322
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0144
AC:
2191
AN:
152328
Hom.:
53
Cov.:
32
AF XY:
0.0140
AC XY:
1040
AN XY:
74500
show subpopulations
Gnomad4 AFR
AF:
0.0495
Gnomad4 AMR
AF:
0.00595
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000235
Gnomad4 OTH
AF:
0.00992
Alfa
AF:
0.00442
Hom.:
4
Bravo
AF:
0.0156
Asia WGS
AF:
0.00260
AC:
10
AN:
3478
EpiCase
AF:
0.000491
EpiControl
AF:
0.000534

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 submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.59
Cadd
Benign
5.3
Dann
Benign
0.65

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs73437462; hg19: chr7-123142735; API