1-156841109-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_014215.3(INSRR):c.3663-5A>G 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 0.000657 in 1,553,406 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_014215.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
INSRR | NM_014215.3 | c.3663-5A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000368195.4 | NP_055030.1 | |||
NTRK1 | NM_001007792.1 | c.10-972T>C | intron_variant | NP_001007793.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
INSRR | ENST00000368195.4 | c.3663-5A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_014215.3 | ENSP00000357178 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00352 AC: 534AN: 151886Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.000838 AC: 136AN: 162388Hom.: 2 AF XY: 0.000594 AC XY: 51AN XY: 85862
GnomAD4 exome AF: 0.000345 AC: 484AN: 1401404Hom.: 5 Cov.: 31 AF XY: 0.000282 AC XY: 195AN XY: 692118
GnomAD4 genome AF: 0.00353 AC: 537AN: 152002Hom.: 2 Cov.: 31 AF XY: 0.00350 AC XY: 260AN XY: 74298
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at