15-90429671-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_003870.4(IQGAP1):c.390+5C>T variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00194 in 1,580,998 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_003870.4 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQGAP1 | NM_003870.4 | c.390+5C>T | splice_donor_5th_base_variant, intron_variant | ENST00000268182.10 | |||
IQGAP1 | XM_047433204.1 | c.390+5C>T | splice_donor_5th_base_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQGAP1 | ENST00000268182.10 | c.390+5C>T | splice_donor_5th_base_variant, intron_variant | 1 | NM_003870.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00827 AC: 1257AN: 152046Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00260 AC: 622AN: 239592Hom.: 7 AF XY: 0.00191 AC XY: 248AN XY: 129844
GnomAD4 exome AF: 0.00126 AC: 1806AN: 1428834Hom.: 21 Cov.: 25 AF XY: 0.00122 AC XY: 869AN XY: 712362
GnomAD4 genome ? AF: 0.00833 AC: 1268AN: 152164Hom.: 11 Cov.: 32 AF XY: 0.00804 AC XY: 598AN XY: 74394
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 18, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at