chr1-185301203-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_006469.5(IVNS1ABP):c.896-7C>T 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 0.00292 in 1,604,110 control chromosomes in the GnomAD database, including 72 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_006469.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IVNS1ABP | NM_006469.5 | c.896-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000367498.8 | |||
IVNS1ABP | XM_047434070.1 | c.896-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
IVNS1ABP | XM_047434096.1 | c.629-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
IVNS1ABP | XM_047434109.1 | c.242-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IVNS1ABP | ENST00000367498.8 | c.896-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006469.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00174 AC: 265AN: 152058Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00462 AC: 1151AN: 249282Hom.: 17 AF XY: 0.00611 AC XY: 824AN XY: 134764
GnomAD4 exome AF: 0.00304 AC: 4418AN: 1451934Hom.: 70 Cov.: 29 AF XY: 0.00387 AC XY: 2800AN XY: 722962
GnomAD4 genome AF: 0.00175 AC: 267AN: 152176Hom.: 2 Cov.: 32 AF XY: 0.00234 AC XY: 174AN XY: 74388
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at