rs148768851
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015634.4(KIFBP):c.68A>G(p.Glu23Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00122 in 1,614,230 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_015634.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIFBP | NM_015634.4 | c.68A>G | p.Glu23Gly | missense_variant | Exon 1 of 7 | ENST00000361983.7 | NP_056449.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00605 AC: 921AN: 152234Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00178 AC: 446AN: 251208Hom.: 2 AF XY: 0.00132 AC XY: 180AN XY: 135862
GnomAD4 exome AF: 0.000720 AC: 1052AN: 1461878Hom.: 13 Cov.: 30 AF XY: 0.000645 AC XY: 469AN XY: 727244
GnomAD4 genome AF: 0.00605 AC: 922AN: 152352Hom.: 8 Cov.: 33 AF XY: 0.00560 AC XY: 417AN XY: 74490
ClinVar
Submissions by phenotype
Goldberg-Shprintzen syndrome Uncertain:1Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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not specified Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:2
KIFBP: BS1, BS2 -
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KIFBP-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at