2-8682268-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_002166.5(ID2):c.103C>T(p.Leu35Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00218 in 1,614,138 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.012 ( 43 hom., cov: 31)
Exomes 𝑓: 0.0012 ( 40 hom. )
Consequence
ID2
NM_002166.5 synonymous
NM_002166.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.69
Genes affected
ID2 (HGNC:5361): (inhibitor of DNA binding 2) The protein encoded by this gene belongs to the inhibitor of DNA binding family, members of which are transcriptional regulators that contain a helix-loop-helix (HLH) domain but not a basic domain. Members of the inhibitor of DNA binding family inhibit the functions of basic helix-loop-helix transcription factors in a dominant-negative manner by suppressing their heterodimerization partners through the HLH domains. This protein may play a role in negatively regulating cell differentiation. A pseudogene of this gene is located on chromosome 3. [provided by RefSeq, Aug 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BP6
Variant 2-8682268-C-T is Benign according to our data. Variant chr2-8682268-C-T is described in ClinVar as [Benign]. Clinvar id is 783971.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.69 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0115 (1757/152328) while in subpopulation AFR AF= 0.0404 (1679/41568). AF 95% confidence interval is 0.0388. There are 43 homozygotes in gnomad4. There are 865 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1757 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ID2 | ENST00000396290.2 | c.103C>T | p.Leu35Leu | synonymous_variant | Exon 1 of 3 | 1 | NM_002166.5 | ENSP00000379585.1 | ||
ID2 | ENST00000234091.8 | c.103C>T | p.Leu35Leu | synonymous_variant | Exon 3 of 5 | 1 | ENSP00000234091.4 | |||
ID2 | ENST00000331129.3 | c.103C>T | p.Leu35Leu | synonymous_variant | Exon 1 of 2 | 1 | ENSP00000385465.2 |
Frequencies
GnomAD3 genomes AF: 0.0115 AC: 1755AN: 152210Hom.: 43 Cov.: 31
GnomAD3 genomes
AF:
AC:
1755
AN:
152210
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:
GnomAD3 exomes AF: 0.00308 AC: 775AN: 251306Hom.: 16 AF XY: 0.00230 AC XY: 312AN XY: 135888
GnomAD3 exomes
AF:
AC:
775
AN:
251306
Hom.:
AF XY:
AC XY:
312
AN XY:
135888
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00121 AC: 1764AN: 1461810Hom.: 40 Cov.: 32 AF XY: 0.000965 AC XY: 702AN XY: 727210
GnomAD4 exome
AF:
AC:
1764
AN:
1461810
Hom.:
Cov.:
32
AF XY:
AC XY:
702
AN XY:
727210
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0115 AC: 1757AN: 152328Hom.: 43 Cov.: 31 AF XY: 0.0116 AC XY: 865AN XY: 74482
GnomAD4 genome
AF:
AC:
1757
AN:
152328
Hom.:
Cov.:
31
AF XY:
AC XY:
865
AN XY:
74482
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
6
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Sep 14, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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