rs200040694
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001127202.4(PCID2):c.1111-4G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000549 in 1,458,124 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001127202.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCID2 | ENST00000337344.9 | c.1111-4G>T | splice_region_variant, intron_variant | Intron 13 of 13 | 2 | NM_001127202.4 | ENSP00000337405.4 | |||
PCID2 | ENST00000375477.5 | c.1111-4G>T | splice_region_variant, intron_variant | Intron 13 of 14 | 1 | ENSP00000364626.1 | ||||
PCID2 | ENST00000375479.6 | c.1111-4G>T | splice_region_variant, intron_variant | Intron 13 of 14 | 2 | ENSP00000364628.2 | ||||
PCID2 | ENST00000375457.2 | c.1105-4G>T | splice_region_variant, intron_variant | Intron 13 of 13 | 1 | ENSP00000364606.2 | ||||
PCID2 | ENST00000375459.5 | c.1105-4G>T | splice_region_variant, intron_variant | Intron 13 of 14 | 2 | ENSP00000364608.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000549 AC: 8AN: 1458124Hom.: 0 Cov.: 28 AF XY: 0.00000689 AC XY: 5AN XY: 725656
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at