chr1-156840887-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014215.3(INSRR):c.3880G>T(p.Gly1294Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,613,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014215.3 missense
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 |
---|---|---|---|---|---|---|---|
INSRR | NM_014215.3 | c.3880G>T | p.Gly1294Cys | missense_variant | 22/22 | ENST00000368195.4 | |
NTRK1 | NM_001007792.1 | c.10-1194C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INSRR | ENST00000368195.4 | c.3880G>T | p.Gly1294Cys | missense_variant | 22/22 | 1 | NM_014215.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152188Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000882 AC: 22AN: 249398Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135038
GnomAD4 exome AF: 0.000105 AC: 154AN: 1460942Hom.: 0 Cov.: 31 AF XY: 0.0000881 AC XY: 64AN XY: 726780
GnomAD4 genome AF: 0.000131 AC: 20AN: 152306Hom.: 0 Cov.: 31 AF XY: 0.000107 AC XY: 8AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2022 | The c.3880G>T (p.G1294C) alteration is located in exon 22 (coding exon 22) of the INSRR gene. This alteration results from a G to T substitution at nucleotide position 3880, causing the glycine (G) at amino acid position 1294 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at