NM_001384355.1:c.1480-670A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001384355.1(RAD21L1):c.1480-670A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0121 in 152,178 control chromosomes in the GnomAD database, including 35 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 0.012 ( 35 hom., cov: 32)
Consequence
RAD21L1
NM_001384355.1 intron
NM_001384355.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.626
Publications
0 publications found
Genes affected
RAD21L1 (HGNC:16271): (RAD21 cohesin complex component like 1) Predicted to enable chromatin binding activity. Predicted to be involved in mitotic sister chromatid cohesion; replication-born double-strand break repair via sister chromatid exchange; and synaptonemal complex assembly. Predicted to act upstream of or within several processes, including double-strand break repair via homologous recombination; homologous chromosome segregation; and seminiferous tubule development. Predicted to be located in lateral element. Predicted to be part of nuclear meiotic cohesin complex and nuclear mitotic cohesin complex. Predicted to be active in synaptonemal complex. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.83).
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0121 (1834/152178) while in subpopulation AFR AF = 0.0425 (1766/41534). AF 95% confidence interval is 0.0409. There are 35 homozygotes in GnomAd4. There are 847 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High AC in GnomAd4 at 1834 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAD21L1 | NM_001384355.1 | c.1480-670A>G | intron_variant | Intron 13 of 13 | ENST00000683101.1 | NP_001371284.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAD21L1 | ENST00000683101.1 | c.1480-670A>G | intron_variant | Intron 13 of 13 | NM_001384355.1 | ENSP00000507397.1 | ||||
RAD21L1 | ENST00000409241.5 | c.1483-670A>G | intron_variant | Intron 13 of 13 | 1 | ENSP00000386414.1 | ||||
RAD21L1 | ENST00000402452.5 | c.1386+4896A>G | intron_variant | Intron 12 of 13 | 5 | ENSP00000385925.1 |
Frequencies
GnomAD3 genomes AF: 0.0121 AC: 1837AN: 152060Hom.: 35 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1837
AN:
152060
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: 0.0121 AC: 1834AN: 152178Hom.: 35 Cov.: 32 AF XY: 0.0114 AC XY: 847AN XY: 74388 show subpopulations
GnomAD4 genome
AF:
AC:
1834
AN:
152178
Hom.:
Cov.:
32
AF XY:
AC XY:
847
AN XY:
74388
show subpopulations
African (AFR)
AF:
AC:
1766
AN:
41534
American (AMR)
AF:
AC:
46
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5170
South Asian (SAS)
AF:
AC:
1
AN:
4816
European-Finnish (FIN)
AF:
AC:
0
AN:
10602
Middle Eastern (MID)
AF:
AC:
3
AN:
294
European-Non Finnish (NFE)
AF:
AC:
3
AN:
67988
Other (OTH)
AF:
AC:
15
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
83
167
250
334
417
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
22
44
66
88
110
<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:
5
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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