rs9940089
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001171.6(ABCC6):c.1338+7C>T variant causes a splice region, 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. 3/3 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_001171.6 splice_region, 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 |
---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.1338+7C>T | splice_region_variant, intron_variant | ENST00000205557.12 | |||
ABCC6 | NM_001351800.1 | c.996+7C>T | splice_region_variant, intron_variant | ||||
ABCC6 | NR_147784.1 | n.1375+7C>T | splice_region_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.1338+7C>T | splice_region_variant, intron_variant | 1 | NM_001171.6 | P1 | |||
ABCC6 | ENST00000574094.6 | c.1338+7C>T | splice_region_variant, intron_variant | 5 | |||||
ABCC6 | ENST00000456970.6 | c.1338+7C>T | splice_region_variant, intron_variant, NMD_transcript_variant | 2 | |||||
ABCC6 | ENST00000622290.5 | c.1338+7C>T | splice_region_variant, intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 28
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.84e-7 AC: 1AN: 1461422Hom.: 0 Cov.: 50 AF XY: 0.00000138 AC XY: 1AN XY: 726974
GnomAD4 genome ? Cov.: 28
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at