NM_001003795.3:c.2628G>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_001003795.3(GTF2IRD2B):c.2628G>A(p.Thr876Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 146,526 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T876T) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0000068 ( 0 hom., cov: 23)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
GTF2IRD2B
NM_001003795.3 synonymous
NM_001003795.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0300
Publications
0 publications found
Genes affected
GTF2IRD2B (HGNC:33125): (GTF2I repeat domain containing 2B) This gene encodes a glycosylated phosphoprotein with a leucine zipper motif, two helix-loop-helix motifs (I repeats) that are similar to domains found in the TFII-I family of transcription factors, one CHARLIE8 transposable element-like sequence, and a BED zinc finger. This gene lies within a region that is deleted in Williams-Beuren syndrome. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP7
Synonymous conserved (PhyloP=-0.03 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001003795.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GTF2IRD2B | TSL:1 MANE Select | c.2628G>A | p.Thr876Thr | synonymous | Exon 16 of 16 | ENSP00000480524.1 | Q6EKJ0-1 | ||
| GTF2IRD2B | TSL:1 | n.*1903G>A | non_coding_transcript_exon | Exon 15 of 15 | ENSP00000411454.3 | Q6EKJ0-2 | |||
| GTF2IRD2B | TSL:1 | n.2316G>A | non_coding_transcript_exon | Exon 10 of 10 |
Frequencies
GnomAD3 genomes 0.00000682 AC: 1AN: 146526Hom.: 0 Cov.: 23 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
146526
Hom.:
Cov.:
23
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:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000142 AC: 1AN: 703854Hom.: 0 Cov.: 9 AF XY: 0.00000264 AC XY: 1AN XY: 378122 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
703854
Hom.:
Cov.:
9
AF XY:
AC XY:
1
AN XY:
378122
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
19248
American (AMR)
AF:
AC:
0
AN:
43814
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
21486
East Asian (EAS)
AF:
AC:
0
AN:
36380
South Asian (SAS)
AF:
AC:
0
AN:
71202
European-Finnish (FIN)
AF:
AC:
0
AN:
53158
Middle Eastern (MID)
AF:
AC:
0
AN:
2692
European-Non Finnish (NFE)
AF:
AC:
1
AN:
420510
Other (OTH)
AF:
AC:
0
AN:
35364
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.325
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000682 AC: 1AN: 146526Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 70936 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
146526
Hom.:
Cov.:
23
AF XY:
AC XY:
0
AN XY:
70936
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
39450
American (AMR)
AF:
AC:
0
AN:
14404
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3436
East Asian (EAS)
AF:
AC:
0
AN:
4902
South Asian (SAS)
AF:
AC:
0
AN:
4442
European-Finnish (FIN)
AF:
AC:
0
AN:
10022
Middle Eastern (MID)
AF:
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
AC:
1
AN:
66694
Other (OTH)
AF:
AC:
0
AN:
1970
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.275
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational 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
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