rs12446956
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000641790.1(LINC01568):n.524-19117T>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 0.104 in 152,216 control chromosomes in the GnomAD database, including 1,146 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
ENST00000641790.1 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 |
---|---|---|---|---|---|---|---|
ZFHX3 | NM_001386735.1 | c.-1063-11379A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01568 | ENST00000641790.1 | n.524-19117T>C | intron_variant, non_coding_transcript_variant | ||||||
ZFHX3 | ENST00000641206.2 | c.-1546-11379A>G | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.104 AC: 15794AN: 152098Hom.: 1147 Cov.: 32
GnomAD4 genome ? AF: 0.104 AC: 15788AN: 152216Hom.: 1146 Cov.: 32 AF XY: 0.107 AC XY: 7991AN XY: 74424
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at