chr22-39091590-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000560933.5(ENSG00000225720):n.5T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 152,736 control chromosomes in the GnomAD database, including 26,538 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC101927202 | XR_938259.3 | n.529T>C | non_coding_transcript_exon_variant | 1/2 | |||
LOC101927202 | XR_007068102.1 | n.125T>C | non_coding_transcript_exon_variant | 2/4 | |||
LOC101927202 | XR_007068103.1 | n.60-17T>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000560933.5 | n.5T>C | non_coding_transcript_exon_variant | 1/2 | ||||||
ENST00000684966.1 | n.126T>C | non_coding_transcript_exon_variant | 2/4 | ||||||
ENST00000424436.2 | n.60-17T>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.559 AC: 84828AN: 151792Hom.: 26327 Cov.: 31
GnomAD4 exome AF: 0.615 AC: 508AN: 826Hom.: 157 Cov.: 0 AF XY: 0.602 AC XY: 277AN XY: 460
GnomAD4 genome AF: 0.559 AC: 84936AN: 151910Hom.: 26381 Cov.: 31 AF XY: 0.557 AC XY: 41304AN XY: 74212
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at