rs745363423
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_001365951.3(KIF1B):c.3245G>A(p.Arg1082Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000378 in 1,613,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1082P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001365951.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF1B | NM_001365951.3 | c.3245G>A | p.Arg1082Gln | missense_variant | 30/49 | ENST00000676179.1 | NP_001352880.1 | |
KIF1B | NM_001365952.1 | c.3245G>A | p.Arg1082Gln | missense_variant | 30/49 | NP_001352881.1 | ||
KIF1B | NM_015074.3 | c.3107G>A | p.Arg1036Gln | missense_variant | 28/47 | NP_055889.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF1B | ENST00000676179.1 | c.3245G>A | p.Arg1082Gln | missense_variant | 30/49 | NM_001365951.3 | ENSP00000502065.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000151 AC: 38AN: 251466Hom.: 0 AF XY: 0.000132 AC XY: 18AN XY: 135902
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1461870Hom.: 0 Cov.: 33 AF XY: 0.0000385 AC XY: 28AN XY: 727238
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74280
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Charcot-Marie-Tooth disease type 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at