GeneBe

chr20-290584-T-TTTAAA

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_153269.3(C20orf96):​c.20+6_20+7insTTTAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000705 in 1,419,056 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 7.0e-7 ( 0 hom. )

Consequence

C20orf96
NM_153269.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.380

Publications

0 publications found
Variant links:
Genes affected
C20orf96 (HGNC:16227): (chromosome 20 open reading frame 96)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
C20orf96NM_153269.3 linkc.20+6_20+7insTTTAA splice_region_variant, intron_variant Intron 1 of 10 ENST00000360321.7 NP_695001.2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C20orf96ENST00000360321.7 linkc.20+6_20+7insTTTAA splice_region_variant, intron_variant Intron 1 of 10 1 NM_153269.3 ENSP00000353470.2
C20orf96ENST00000400269.4 linkc.17+2_17+3insTTTAA splice_donor_variant, intron_variant Intron 1 of 10 1 ENSP00000383128.4
C20orf96ENST00000382369.9 linkc.-245_-244insTTTAA upstream_gene_variant 5 ENSP00000371806.5

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
7.05e-7
AC:
1
AN:
1419056
Hom.:
0
Cov.:
36
AF XY:
0.00
AC XY:
0
AN XY:
705200
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
30936
American (AMR)
AF:
0.00
AC:
0
AN:
38758
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25202
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38730
South Asian (SAS)
AF:
0.00
AC:
0
AN:
81278
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
48508
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5180
European-Non Finnish (NFE)
AF:
9.16e-7
AC:
1
AN:
1091810
Other (OTH)
AF:
0.00
AC:
0
AN:
58654
⚠️ 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: 0.275
Heterozygous variant carriers
0
0
1
1
2
2
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
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.38

Splicing

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

Publications

Other links and lift over

dbSNP: rs3835237; hg19: chr20-271225; API