chr6-75922180-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001563.4(IMPG1):c.2317-14T>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000995 in 1,004,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001563.4 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IMPG1 | NM_001563.4 | c.2317-14T>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000369950.8 | |||
IMPG1 | NM_001282368.2 | c.2083-14T>G | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IMPG1 | ENST00000369950.8 | c.2317-14T>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001563.4 | P2 | |||
IMPG1 | ENST00000369952.3 | c.400-14T>G | splice_polypyrimidine_tract_variant, intron_variant | 3 | |||||
IMPG1 | ENST00000611179.4 | c.2083-14T>G | splice_polypyrimidine_tract_variant, intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 9.95e-7 AC: 1AN: 1004972Hom.: 0 Cov.: 14 AF XY: 0.00000195 AC XY: 1AN XY: 513726
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 04, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.