3-51830503-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001393887.1(IQCF3):c.167C>A(p.Ala56Asp) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,592 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A56P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001393887.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQCF3 | NM_001393887.1 | c.167C>A | p.Ala56Asp | missense_variant | 3/3 | ENST00000440739.4 | |
IQCF3 | NM_001085479.3 | c.167C>A | p.Ala56Asp | missense_variant | 7/7 | ||
IQCF3 | NM_001207023.2 | c.167C>A | p.Ala56Asp | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCF3 | ENST00000440739.4 | c.167C>A | p.Ala56Asp | missense_variant | 3/3 | 2 | NM_001393887.1 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248966Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135010
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461592Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727080
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 12, 2024 | The c.167C>A (p.A56D) alteration is located in exon 7 (coding exon 3) of the IQCF3 gene. This alteration results from a C to A substitution at nucleotide position 167, causing the alanine (A) at amino acid position 56 to be replaced by an aspartic acid (D). 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