chr6-31062447-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000805383.1(HCG22):n.734-1562C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0224 in 152,188 control chromosomes in the GnomAD database, including 68 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 0.022 ( 68 hom., cov: 32)
Consequence
HCG22
ENST00000805383.1 intron
ENST00000805383.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0740
Publications
15 publications found
Genes affected
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=-0.92).
BS1
Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0224 (3404/152188) while in subpopulation AMR AF = 0.0396 (605/15272). AF 95% confidence interval is 0.037. There are 68 homozygotes in GnomAd4. There are 1550 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 68 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0224 AC: 3404AN: 152070Hom.: 68 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
3404
AN:
152070
Hom.:
Cov.:
32
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0224 AC: 3404AN: 152188Hom.: 68 Cov.: 32 AF XY: 0.0208 AC XY: 1550AN XY: 74402 show subpopulations
GnomAD4 genome
AF:
AC:
3404
AN:
152188
Hom.:
Cov.:
32
AF XY:
AC XY:
1550
AN XY:
74402
show subpopulations
African (AFR)
AF:
AC:
1187
AN:
41520
American (AMR)
AF:
AC:
605
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
380
AN:
3472
East Asian (EAS)
AF:
AC:
1
AN:
5182
South Asian (SAS)
AF:
AC:
11
AN:
4814
European-Finnish (FIN)
AF:
AC:
13
AN:
10596
Middle Eastern (MID)
AF:
AC:
6
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1123
AN:
68014
Other (OTH)
AF:
AC:
75
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
164
327
491
654
818
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
36
72
108
144
180
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
11
AN:
3478
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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