rs16960453
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000662551.1(ENSG00000259754):n.189-1770C>A 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 0.0000328 in 152,208 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC124900354 | XR_001751516.3 | n.143-1770C>A | intron_variant, non_coding_transcript_variant | |||||
LOC102724553 | XR_001751520.2 | n.263-3085G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENST00000662551.1 | n.189-1770C>A | intron_variant, non_coding_transcript_variant | ||||||||
ENST00000560900.1 | n.196-1770C>A | intron_variant, non_coding_transcript_variant | 4 | |||||||
ENST00000664705.1 | n.189-1770C>A | intron_variant, non_coding_transcript_variant | ||||||||
ENST00000665188.1 | n.69-1770C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152090Hom.: 0 Cov.: 32
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74414
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at