rs10934657
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001388419.1(KALRN):c.73+60176T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
KALRN
NM_001388419.1 intron
NM_001388419.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.636
Publications
3 publications found
Genes affected
KALRN (HGNC:4814): (kalirin RhoGEF kinase) Huntington's disease (HD), a neurodegenerative disorder characterized by loss of striatal neurons, is caused by an expansion of a polyglutamine tract in the HD protein huntingtin. This gene encodes a protein that interacts with the huntingtin-associated protein 1, which is a huntingtin binding protein that may function in vesicle trafficking. [provided by RefSeq, Apr 2016]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| KALRN | NM_001388419.1 | c.73+60176T>A | intron_variant | Intron 1 of 59 | ENST00000682506.1 | NP_001375348.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| KALRN | ENST00000682506.1 | c.73+60176T>A | intron_variant | Intron 1 of 59 | NM_001388419.1 | ENSP00000508359.1 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 151706Hom.: 0 Cov.: 31
GnomAD3 genomes
AF:
AC:
0
AN:
151706
Hom.:
Cov.:
31
Gnomad AFR
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 108Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 70
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
108
Hom.:
AF XY:
AC XY:
0
AN XY:
70
African (AFR)
AF:
AC:
0
AN:
2
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
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0
South Asian (SAS)
AC:
0
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0
European-Finnish (FIN)
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0
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44
Middle Eastern (MID)
AC:
0
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0
European-Non Finnish (NFE)
AF:
AC:
0
AN:
58
Other (OTH)
AF:
AC:
0
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4
GnomAD4 genome 0.00 AC: 0AN: 151706Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74078
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
151706
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
74078
African (AFR)
AF:
AC:
0
AN:
41170
American (AMR)
AF:
AC:
0
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3462
East Asian (EAS)
AF:
AC:
0
AN:
5150
South Asian (SAS)
AF:
AC:
0
AN:
4818
European-Finnish (FIN)
AF:
AC:
0
AN:
10562
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67970
Other (OTH)
AF:
AC:
0
AN:
2082
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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