chr3-51894993-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152397.3(IQCF1):āc.515A>Gā(p.Gln172Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000688 in 1,614,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_152397.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQCF1 | NM_152397.3 | c.515A>G | p.Gln172Arg | missense_variant | 4/4 | ENST00000310914.10 | |
IQCF1 | XM_011533366.2 | c.410A>G | p.Gln137Arg | missense_variant | 3/3 | ||
IQCF1 | XM_017005729.1 | c.410A>G | p.Gln137Arg | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCF1 | ENST00000310914.10 | c.515A>G | p.Gln172Arg | missense_variant | 4/4 | 1 | NM_152397.3 | P1 | |
IQCF1 | ENST00000314534.6 | c.*436A>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251480Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135920
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.0000619 AC XY: 45AN XY: 727248
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | The c.515A>G (p.Q172R) alteration is located in exon 4 (coding exon 4) of the IQCF1 gene. This alteration results from a A to G substitution at nucleotide position 515, causing the glutamine (Q) at amino acid position 172 to be replaced by an arginine (R). 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