chr6-29972108-G-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0000042 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MICD
intragenic
intragenic
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.203
Publications
5 publications found
Genes affected
MICD (HGNC:7093): (MHC class I polypeptide-related sequence D (pseudogene))
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000413248.1. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MICD | ENST00000413248.1 | TSL:6 | n.256+101C>G | intron | N/A | ||||
| POLR1HASP | ENST00000849678.1 | n.589-25192C>G | intron | N/A | |||||
| POLR1HASP | ENST00000849679.1 | n.65+4495C>G | intron | N/A |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 151652Hom.: 0 Cov.: 30
GnomAD3 genomes
AF:
AC:
0
AN:
151652
Hom.:
Cov.:
30
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 AF: 0.00000416 AC: 1AN: 240576Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 124810 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
240576
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
124810
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:
7424
American (AMR)
AF:
AC:
0
AN:
11632
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
7904
East Asian (EAS)
AF:
AC:
0
AN:
17846
South Asian (SAS)
AF:
AC:
0
AN:
17506
European-Finnish (FIN)
AF:
AC:
0
AN:
15114
Middle Eastern (MID)
AF:
AC:
0
AN:
1178
European-Non Finnish (NFE)
AF:
AC:
1
AN:
147044
Other (OTH)
AF:
AC:
0
AN:
14928
⚠️ 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: 0.225
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 0.00 AC: 0AN: 151652Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74024
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
151652
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
74024
African (AFR)
AF:
AC:
0
AN:
41216
American (AMR)
AF:
AC:
0
AN:
15246
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3464
East Asian (EAS)
AF:
AC:
0
AN:
5152
South Asian (SAS)
AF:
AC:
0
AN:
4806
European-Finnish (FIN)
AF:
AC:
0
AN:
10518
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67938
Other (OTH)
AF:
AC:
0
AN:
2086
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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