3-12899391-TAGG-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PM4_SupportingBP6
The NM_014869.8(IQSEC1):c.2888_2890delCCT(p.Ser963del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000102 in 1,612,962 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_014869.8 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IQSEC1 | ENST00000273221.8 | c.2888_2890delCCT | p.Ser963del | disruptive_inframe_deletion | Exon 14 of 14 | 1 | ENSP00000273221.4 | |||
IQSEC1 | ENST00000613206 | c.*1589_*1591delCCT | 3_prime_UTR_variant | Exon 14 of 14 | 2 | NM_001134382.3 | ENSP00000480301.1 | |||
IQSEC1 | ENST00000646269.1 | c.2891_2893delCCT | p.Ser964del | disruptive_inframe_deletion | Exon 14 of 14 | ENSP00000496366.1 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000356 AC: 88AN: 247484Hom.: 0 AF XY: 0.000342 AC XY: 46AN XY: 134510
GnomAD4 exome AF: 0.0000965 AC: 141AN: 1460718Hom.: 0 AF XY: 0.0000881 AC XY: 64AN XY: 726630
GnomAD4 genome AF: 0.000151 AC: 23AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74382
ClinVar
Submissions by phenotype
IQSEC1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at