1-156841712-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_014215.3(INSRR):c.3480C>T(p.Ala1160Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000658 in 1,614,118 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0032 ( 4 hom., cov: 31)
Exomes 𝑓: 0.00039 ( 4 hom. )
Consequence
INSRR
NM_014215.3 synonymous
NM_014215.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.315
Publications
1 publications found
Genes affected
INSRR (HGNC:6093): (insulin receptor related receptor) Enables transmembrane receptor protein tyrosine kinase activity. Involved in actin cytoskeleton reorganization; cellular response to alkaline pH; and protein autophosphorylation. Part of receptor complex. [provided by Alliance of Genome Resources, Apr 2022]
NTRK1 (HGNC:8031): (neurotrophic receptor tyrosine kinase 1) This gene encodes a member of the neurotrophic tyrosine kinase receptor (NTKR) family. This kinase is a membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. The presence of this kinase leads to cell differentiation and may play a role in specifying sensory neuron subtypes. Mutations in this gene have been associated with congenital insensitivity to pain, anhidrosis, self-mutilating behavior, cognitive disability and cancer. Alternate transcriptional splice variants of this gene have been found, but only three have been characterized to date. [provided by RefSeq, Jul 2008]
NTRK1 Gene-Disease associations (from GenCC):
- hereditary sensory and autonomic neuropathy type 4Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, ClinGen, Labcorp Genetics (formerly Invitae)
- familial medullary thyroid carcinomaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant 1-156841712-G-A is Benign according to our data. Variant chr1-156841712-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3025245.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.315 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 4 Unknown gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00317 AC: 483AN: 152126Hom.: 4 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
483
AN:
152126
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.000871 AC: 219AN: 251348 AF XY: 0.000581 show subpopulations
GnomAD2 exomes
AF:
AC:
219
AN:
251348
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000393 AC: 575AN: 1461874Hom.: 4 Cov.: 33 AF XY: 0.000364 AC XY: 265AN XY: 727248 show subpopulations
GnomAD4 exome
AF:
AC:
575
AN:
1461874
Hom.:
Cov.:
33
AF XY:
AC XY:
265
AN XY:
727248
show subpopulations
African (AFR)
AF:
AC:
432
AN:
33480
American (AMR)
AF:
AC:
15
AN:
44722
Ashkenazi Jewish (ASJ)
AF:
AC:
13
AN:
26134
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
5
AN:
86256
European-Finnish (FIN)
AF:
AC:
0
AN:
53418
Middle Eastern (MID)
AF:
AC:
17
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
29
AN:
1112002
Other (OTH)
AF:
AC:
64
AN:
60394
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.465
Heterozygous variant carriers
0
35
70
105
140
175
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.00320 AC: 487AN: 152244Hom.: 4 Cov.: 31 AF XY: 0.00310 AC XY: 231AN XY: 74426 show subpopulations
GnomAD4 genome
AF:
AC:
487
AN:
152244
Hom.:
Cov.:
31
AF XY:
AC XY:
231
AN XY:
74426
show subpopulations
African (AFR)
AF:
AC:
467
AN:
41538
American (AMR)
AF:
AC:
10
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
AC:
2
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5178
South Asian (SAS)
AF:
AC:
0
AN:
4820
European-Finnish (FIN)
AF:
AC:
0
AN:
10612
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
3
AN:
68006
Other (OTH)
AF:
AC:
5
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
24
47
71
94
118
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
8
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Sep 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
INSRR: BP4, BP7, BS1 -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.