chr3-124667095-T-C
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001388419.1(KALRN):āc.6615T>Cā(p.Val2205=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0274 in 1,613,910 control chromosomes in the GnomAD database, including 834 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: š 0.028 ( 81 hom., cov: 32)
Exomes š: 0.027 ( 753 hom. )
Consequence
KALRN
NM_001388419.1 synonymous
NM_001388419.1 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0870
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 made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP7
Synonymous conserved (PhyloP=-0.087 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0725 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KALRN | NM_001388419.1 | c.6615T>C | p.Val2205= | synonymous_variant | 47/60 | ENST00000682506.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KALRN | ENST00000682506.1 | c.6615T>C | p.Val2205= | synonymous_variant | 47/60 | NM_001388419.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0277 AC: 4222AN: 152208Hom.: 79 Cov.: 32
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GnomAD3 exomes AF: 0.0318 AC: 7986AN: 251264Hom.: 199 AF XY: 0.0313 AC XY: 4250AN XY: 135794
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GnomAD4 exome AF: 0.0273 AC: 39941AN: 1461584Hom.: 753 Cov.: 31 AF XY: 0.0274 AC XY: 19912AN XY: 727086
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GnomAD4 genome AF: 0.0278 AC: 4241AN: 152326Hom.: 81 Cov.: 32 AF XY: 0.0280 AC XY: 2089AN XY: 74490
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Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at