GeneBe

chr6-30416022-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.163 in 152,734 control chromosomes in the GnomAD database, including 2,213 homozygotes. 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 0.16 ( 2206 hom., cov: 33)
Exomes 𝑓: 0.11 ( 7 hom. )

Consequence

MICC
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.959

Publications

15 publications found
Variant links:
Genes affected
MICC (HGNC:7092): (MHC class I polypeptide-related sequence C (pseudogene))

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MICC n.30416022G>A intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MICCENST00000445710.1 linkn.538-97G>A intron_variant Intron 2 of 4 6

Frequencies

GnomAD3 genomes
AF:
0.163
AC:
24765
AN:
152146
Hom.:
2205
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.238
Gnomad AMI
AF:
0.147
Gnomad AMR
AF:
0.106
Gnomad ASJ
AF:
0.134
Gnomad EAS
AF:
0.0317
Gnomad SAS
AF:
0.139
Gnomad FIN
AF:
0.0891
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.155
Gnomad OTH
AF:
0.153
GnomAD4 exome
AF:
0.113
AC:
53
AN:
470
Hom.:
7
AF XY:
0.122
AC XY:
37
AN XY:
304
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
0.0208
AC:
1
AN:
48
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
0.250
AC:
1
AN:
4
South Asian (SAS)
AF:
0.100
AC:
1
AN:
10
European-Finnish (FIN)
AF:
0.0714
AC:
1
AN:
14
Middle Eastern (MID)
AF:
0.167
AC:
1
AN:
6
European-Non Finnish (NFE)
AF:
0.124
AC:
47
AN:
378
Other (OTH)
AF:
0.100
AC:
1
AN:
10
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.460
Heterozygous variant carriers
0
1
3
4
6
7
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.163
AC:
24779
AN:
152264
Hom.:
2206
Cov.:
33
AF XY:
0.158
AC XY:
11772
AN XY:
74460
show subpopulations
African (AFR)
AF:
0.238
AC:
9882
AN:
41520
American (AMR)
AF:
0.106
AC:
1626
AN:
15310
Ashkenazi Jewish (ASJ)
AF:
0.134
AC:
465
AN:
3472
East Asian (EAS)
AF:
0.0320
AC:
166
AN:
5186
South Asian (SAS)
AF:
0.141
AC:
679
AN:
4822
European-Finnish (FIN)
AF:
0.0891
AC:
946
AN:
10618
Middle Eastern (MID)
AF:
0.0952
AC:
28
AN:
294
European-Non Finnish (NFE)
AF:
0.155
AC:
10532
AN:
68016
Other (OTH)
AF:
0.152
AC:
321
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1078
2155
3233
4310
5388
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
260
520
780
1040
1300
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.158
Hom.:
1395
Bravo
AF:
0.170
Asia WGS
AF:
0.0740
AC:
256
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
7.8
DANN
Benign
0.38
PhyloP100
0.96

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs9261855; hg19: chr6-30383799; API