rs11920543
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001023570.4(IQCB1):c.1303C>T(p.Arg435Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0119 in 1,613,480 control chromosomes in the GnomAD database, including 264 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R435H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001023570.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQCB1 | NM_001023570.4 | c.1303C>T | p.Arg435Cys | missense_variant | 13/15 | ENST00000310864.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCB1 | ENST00000310864.11 | c.1303C>T | p.Arg435Cys | missense_variant | 13/15 | 1 | NM_001023570.4 | P1 | |
IQCB1 | ENST00000349820.10 | c.904C>T | p.Arg302Cys | missense_variant | 10/12 | 1 | |||
IQCB1 | ENST00000393650.7 | c.*281C>T | 3_prime_UTR_variant, NMD_transcript_variant | 12/14 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0111 AC: 1680AN: 151954Hom.: 17 Cov.: 31
GnomAD3 exomes AF: 0.0139 AC: 3501AN: 251390Hom.: 75 AF XY: 0.0134 AC XY: 1814AN XY: 135862
GnomAD4 exome AF: 0.0120 AC: 17566AN: 1461406Hom.: 247 Cov.: 32 AF XY: 0.0115 AC XY: 8360AN XY: 727042
GnomAD4 genome ? AF: 0.0110 AC: 1679AN: 152074Hom.: 17 Cov.: 31 AF XY: 0.0128 AC XY: 952AN XY: 74310
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Senior-Loken syndrome 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Nephronophthisis Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 31, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at