rs2220511
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001100420.2(C21orf91):c.*821G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,896 control chromosomes in the GnomAD database, including 9,337 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 0.34 ( 9337 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
C21orf91
NM_001100420.2 3_prime_UTR
NM_001100420.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.225
Genes affected
C21orf91 (HGNC:16459): (chromosome 21 open reading frame 91) Predicted to be involved in cerebral cortex neuron differentiation and positive regulation of dendritic spine development. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C21orf91 | NM_001100420.2 | c.*821G>A | 3_prime_UTR_variant | 5/5 | ENST00000284881.9 | ||
LOC124900465 | XR_007067823.1 | n.1605+35805C>T | intron_variant, non_coding_transcript_variant | ||||
C21orf91 | NM_001100421.2 | c.*986G>A | 3_prime_UTR_variant | 4/4 | |||
C21orf91 | NM_017447.4 | c.*821G>A | 3_prime_UTR_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C21orf91 | ENST00000284881.9 | c.*821G>A | 3_prime_UTR_variant | 5/5 | 2 | NM_001100420.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.335 AC: 50882AN: 151778Hom.: 9324 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
50882
AN:
151778
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:
GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome ? AF: 0.335 AC: 50936AN: 151896Hom.: 9337 Cov.: 32 AF XY: 0.331 AC XY: 24568AN XY: 74224
GnomAD4 genome
?
AF:
AC:
50936
AN:
151896
Hom.:
Cov.:
32
AF XY:
AC XY:
24568
AN XY:
74224
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1241
AN:
3470
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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