chr11-111299891-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 4P and 6B. PVS1_StrongBP6_ModerateBS2
The ENST00000638573.1(POU2AF3):c.112+1G>A variant causes a splice donor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00981 in 477,620 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000638573.1 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POU2AF3 | NM_001271458.2 | c.8-636G>A | intron_variant | ENST00000610738.6 | |||
COLCA1 | NR_169237.1 | n.222-1225C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POU2AF3 | ENST00000610738.6 | c.8-636G>A | intron_variant | 1 | NM_001271458.2 | P2 | |||
COLCA1 | ENST00000620864.1 | n.219-1225C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00804 AC: 1223AN: 152056Hom.: 10 Cov.: 33
GnomAD4 exome AF: 0.0106 AC: 3464AN: 325444Hom.: 19 Cov.: 5 AF XY: 0.0112 AC XY: 1814AN XY: 162504
GnomAD4 genome AF: 0.00804 AC: 1223AN: 152176Hom.: 10 Cov.: 33 AF XY: 0.00733 AC XY: 545AN XY: 74398
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | COLCA1: BS1, BS2; POU2AF3: BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at