21-17789372-C-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001100420.2(C21orf91):​c.*4043G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Consequence

C21orf91
NM_001100420.2 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.851
Variant links:
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]
C21orf91-OT1 (HGNC:16729): (C21orf91 overlapping transcript 1)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
C21orf91NM_001100420.2 linkc.*4043G>T 3_prime_UTR_variant Exon 5 of 5 ENST00000284881.9 NP_001093890.1 Q9NYK6-1Q68DA1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C21orf91ENST00000284881 linkc.*4043G>T 3_prime_UTR_variant Exon 5 of 5 2 NM_001100420.2 ENSP00000284881.4 Q9NYK6-1
C21orf91-OT1ENST00000430401.5 linkn.34-2162G>T intron_variant Intron 1 of 2 1
C21orf91-OT1ENST00000439392.1 linkn.34-2162G>T intron_variant Intron 1 of 3 1
C21orf91-OT1ENST00000430815.5 linkn.48-2162G>T intron_variant Intron 1 of 4 5

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
0.17
DANN
Benign
0.52

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs243609; hg19: chr21-19161689; API