6-7888855-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030810.5(TXNDC5):c.820-7T>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_030810.5 splice_region, splice_polypyrimidine_tract, intron
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 |
---|---|---|---|---|---|---|---|
TXNDC5 | NM_030810.5 | c.820-7T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000379757.9 | |||
BLOC1S5-TXNDC5 | NR_037616.1 | n.979-7T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | ||||
TXNDC5 | NM_001145549.4 | c.496-7T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNDC5 | ENST00000379757.9 | c.820-7T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_030810.5 | P1 | |||
TXNDC5 | ENST00000473453.2 | c.496-7T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
TXNDC5 | ENST00000460138.5 | n.591T>A | non_coding_transcript_exon_variant | 1/4 | 2 | ||||
TXNDC5 | ENST00000475802.1 | n.107T>A | non_coding_transcript_exon_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1448332Hom.: 0 Cov.: 42 AF XY: 0.00 AC XY: 0AN XY: 719404
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at