7-1471229-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080453.3(INTS1):c.6256-5G>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000343 in 1,572,326 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080453.3 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 |
---|---|---|---|---|---|---|---|
INTS1 | NM_001080453.3 | c.6256-5G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000404767.8 | |||
INTS1 | XM_011515260.2 | c.6286-5G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INTS1 | ENST00000404767.8 | c.6256-5G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001080453.3 | P1 | |||
INTS1 | ENST00000483196.1 | c.295-5G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
INTS1 | ENST00000479671.1 | n.192-5G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 | |||||
INTS1 | ENST00000493446.1 | n.240-5G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152232Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000507 AC: 9AN: 177454Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 95494
GnomAD4 exome AF: 0.0000148 AC: 21AN: 1420094Hom.: 0 Cov.: 31 AF XY: 0.00000854 AC XY: 6AN XY: 702512
GnomAD4 genome AF: 0.000217 AC: 33AN: 152232Hom.: 0 Cov.: 34 AF XY: 0.000202 AC XY: 15AN XY: 74372
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | AiLife Diagnostics, AiLife Diagnostics | Jun 29, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at