16-80549511-A-C
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_130897.3(DYNLRB2):āc.107A>Cā(p.Asn36Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,610,900 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000026 ( 0 hom., cov: 33)
Exomes š: 0.000021 ( 0 hom. )
Consequence
DYNLRB2
NM_130897.3 missense
NM_130897.3 missense
Scores
2
4
10
Clinical Significance
Conservation
PhyloP100: 7.37
Genes affected
DYNLRB2 (HGNC:15467): (dynein light chain roadblock-type 2) Predicted to enable dynein intermediate chain binding activity. Predicted to be involved in microtubule-based movement. Predicted to be located in ciliary tip. Predicted to be part of cytoplasmic dynein complex. Predicted to be active in centrosome and cytoplasm. Biomarker of hepatocellular carcinoma. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.16999003).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYNLRB2 | NM_130897.3 | c.107A>C | p.Asn36Thr | missense_variant | 3/4 | ENST00000305904.11 | |
DYNLRB2-AS1 | NR_120307.1 | n.107+13518T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYNLRB2 | ENST00000305904.11 | c.107A>C | p.Asn36Thr | missense_variant | 3/4 | 1 | NM_130897.3 | P1 | |
ENST00000568275.1 | n.192-1327T>G | intron_variant, non_coding_transcript_variant | 4 | ||||||
DYNLRB2-AS1 | ENST00000668341.1 | n.272+13518T>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152214Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000120 AC: 30AN: 250562Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135434
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GnomAD4 exome AF: 0.0000213 AC: 31AN: 1458686Hom.: 0 Cov.: 30 AF XY: 0.0000262 AC XY: 19AN XY: 725502
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74378
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.107A>C (p.N36T) alteration is located in exon 3 (coding exon 3) of the DYNLRB2 gene. This alteration results from a A to C substitution at nucleotide position 107, causing the asparagine (N) at amino acid position 36 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
0.84
.;P
Vest4
MutPred
0.42
.;Gain of glycosylation at S37 (P = 0.0849);
MVP
MPC
0.022
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at