chr1-156841048-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014215.3(INSRR):c.3719C>T(p.Thr1240Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000992 in 1,593,166 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
INSRR | NM_014215.3 | c.3719C>T | p.Thr1240Ile | missense_variant | 22/22 | ENST00000368195.4 | NP_055030.1 | |
NTRK1 | NM_001007792.1 | c.10-1033G>A | intron_variant | NP_001007793.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
INSRR | ENST00000368195.4 | c.3719C>T | p.Thr1240Ile | missense_variant | 22/22 | 1 | NM_014215.3 | ENSP00000357178 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152220Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000125 AC: 26AN: 208036Hom.: 0 AF XY: 0.000107 AC XY: 12AN XY: 112034
GnomAD4 exome AF: 0.000101 AC: 146AN: 1440828Hom.: 0 Cov.: 32 AF XY: 0.000101 AC XY: 72AN XY: 714744
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152338Hom.: 0 Cov.: 31 AF XY: 0.0000671 AC XY: 5AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 23, 2023 | The c.3719C>T (p.T1240I) alteration is located in exon 22 (coding exon 22) of the INSRR gene. This alteration results from a C to T substitution at nucleotide position 3719, causing the threonine (T) at amino acid position 1240 to be replaced by an isoleucine (I). 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