X-65595656-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000609205.5(MSN):n.539+5887C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 112,042 control chromosomes in the GnomAD database, including 7,495 homozygotes. There are 7,382 hemizygotes in GnomAD. 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
Consequence
ENST00000609205.5 intron, non_coding_transcript
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 |
---|---|---|---|---|---|---|---|
MSN | XM_005262269.3 | c.15+7044C>T | intron_variant | ||||
MSN | XM_011530959.1 | c.111+6588C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSN | ENST00000609205.5 | n.539+5887C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
MSN | ENST00000609672.5 | c.-22+7044C>T | intron_variant | 4 | |||||
MSN | ENST00000429601.1 | n.399-5006C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.236 AC: 26409AN: 111992Hom.: 7487 Cov.: 23 AF XY: 0.215 AC XY: 7338AN XY: 34168
GnomAD4 genome AF: 0.236 AC: 26472AN: 112042Hom.: 7495 Cov.: 23 AF XY: 0.216 AC XY: 7382AN XY: 34228
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at