3-121770379-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001023570.4(IQCB1):āc.1763A>Cā(p.Glu588Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001023570.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IQCB1 | NM_001023570.4 | c.1763A>C | p.Glu588Ala | missense_variant | 15/15 | ENST00000310864.11 | NP_001018864.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IQCB1 | ENST00000310864.11 | c.1763A>C | p.Glu588Ala | missense_variant | 15/15 | 1 | NM_001023570.4 | ENSP00000311505.6 | ||
IQCB1 | ENST00000349820.10 | c.1364A>C | p.Glu455Ala | missense_variant | 12/12 | 1 | ENSP00000323756.7 | |||
IQCB1 | ENST00000393650.7 | n.*741A>C | non_coding_transcript_exon_variant | 14/14 | 5 | ENSP00000377261.3 | ||||
IQCB1 | ENST00000393650.7 | n.*741A>C | 3_prime_UTR_variant | 14/14 | 5 | ENSP00000377261.3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461570Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727130
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74376
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2021 | The c.1763A>C (p.E588A) alteration is located in exon 15 (coding exon 13) of the IQCB1 gene. This alteration results from a A to C substitution at nucleotide position 1763, causing the glutamic acid (E) at amino acid position 588 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at