rs41275792
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NR_108100.1(SPACA6-AS1):n.543C>G 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 0.000895 in 529,612 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
Consequence
NR_108100.1 non_coding_transcript_exon
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 | UniProt |
---|---|---|---|---|---|---|---|
SPACA6-AS1 | NR_108100.1 | n.543C>G | non_coding_transcript_exon_variant | 1/2 | |||
SPACA6 | NM_001316994.2 | c.92-1564G>C | intron_variant | ||||
SPACA6 | XM_017026300.3 | c.-41-1564G>C | intron_variant | ||||
MIRLET7E | NR_029482.1 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPACA6-AS1 | ENST00000602324.1 | n.543C>G | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
SPACA6 | ENST00000646845.1 | c.368-1564G>C | intron_variant | ||||||
SPACA6 | ENST00000710615.1 | c.-41-1564G>C | intron_variant | A2 | |||||
MIRLET7E | ENST00000362102.3 | downstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000789 AC: 120AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000831 AC: 199AN: 239550Hom.: 0 AF XY: 0.000944 AC XY: 123AN XY: 130264
GnomAD4 exome AF: 0.000938 AC: 354AN: 377506Hom.: 0 Cov.: 0 AF XY: 0.00101 AC XY: 217AN XY: 214630
GnomAD4 genome ? AF: 0.000789 AC: 120AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.000902 AC XY: 67AN XY: 74314
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at