NM_030806.4:c.-124-44012A>G

Variant summary

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

The NM_030806.4(C1orf21):​c.-124-44012A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,200 control chromosomes in the GnomAD database, including 1,845 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 0.15 ( 1845 hom., cov: 32)

Consequence

C1orf21
NM_030806.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.242

Publications

2 publications found
Variant links:
Genes affected
C1orf21 (HGNC:15494): (chromosome 1 open reading frame 21)

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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
C1orf21NM_030806.4 linkc.-124-44012A>G intron_variant Intron 1 of 5 ENST00000235307.7 NP_110433.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C1orf21ENST00000235307.7 linkc.-124-44012A>G intron_variant Intron 1 of 5 1 NM_030806.4 ENSP00000235307.6 Q9H246
C1orf21ENST00000648109.1 linkn.-124-44012A>G intron_variant Intron 1 of 6 ENSP00000498051.1 A0A3B3ITU3
C1orf21ENST00000675061.1 linkn.-124-44012A>G intron_variant Intron 1 of 5 ENSP00000501948.1 A0A6Q8PFS2

Frequencies

GnomAD3 genomes
AF:
0.153
AC:
23214
AN:
152082
Hom.:
1843
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.175
Gnomad AMI
AF:
0.224
Gnomad AMR
AF:
0.150
Gnomad ASJ
AF:
0.160
Gnomad EAS
AF:
0.153
Gnomad SAS
AF:
0.114
Gnomad FIN
AF:
0.140
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.143
Gnomad OTH
AF:
0.163
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.153
AC:
23240
AN:
152200
Hom.:
1845
Cov.:
32
AF XY:
0.151
AC XY:
11245
AN XY:
74432
show subpopulations
African (AFR)
AF:
0.175
AC:
7250
AN:
41528
American (AMR)
AF:
0.151
AC:
2299
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
0.160
AC:
554
AN:
3470
East Asian (EAS)
AF:
0.153
AC:
795
AN:
5186
South Asian (SAS)
AF:
0.114
AC:
550
AN:
4822
European-Finnish (FIN)
AF:
0.140
AC:
1490
AN:
10610
Middle Eastern (MID)
AF:
0.153
AC:
45
AN:
294
European-Non Finnish (NFE)
AF:
0.143
AC:
9710
AN:
68002
Other (OTH)
AF:
0.162
AC:
343
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1019
2039
3058
4078
5097
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
244
488
732
976
1220
<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:
0.107
Hom.:
218
Bravo
AF:
0.153
Asia WGS
AF:
0.135
AC:
471
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.4
DANN
Benign
0.45
PhyloP100
0.24
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs16823149; hg19: chr1-184402508; API