chr1-19517082-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XR_947017.3(LOC105376817):n.293+1001T>C 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 0.177 in 152,126 control chromosomes in the GnomAD database, including 2,610 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
Consequence
XR_947017.3 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 |
---|---|---|---|---|---|---|---|
LOC105376817 | XR_947017.3 | n.293+1001T>C | intron_variant, non_coding_transcript_variant | ||||
LOC105376819 | XR_001737920.2 | n.144-1039A>G | intron_variant, non_coding_transcript_variant | ||||
LOC105376819 | XR_947019.1 | n.189-1039A>G | intron_variant, non_coding_transcript_variant | ||||
LOC105376819 | XR_947020.3 | n.144-1039A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICOS10 | ENST00000648702.1 | c.-54+32427A>G | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.177 AC: 26847AN: 152008Hom.: 2607 Cov.: 32
GnomAD4 genome AF: 0.177 AC: 26875AN: 152126Hom.: 2610 Cov.: 32 AF XY: 0.172 AC XY: 12824AN XY: 74394
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at