rs149276487
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015346.4(ZFYVE26):c.4066T>G(p.Cys1356Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000668 in 1,613,060 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_015346.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00122 AC: 186AN: 152014Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00200 AC: 500AN: 250552Hom.: 10 AF XY: 0.00185 AC XY: 251AN XY: 135464
GnomAD4 exome AF: 0.000610 AC: 891AN: 1460926Hom.: 24 Cov.: 34 AF XY: 0.000553 AC XY: 402AN XY: 726612
GnomAD4 genome AF: 0.00123 AC: 187AN: 152134Hom.: 6 Cov.: 33 AF XY: 0.000995 AC XY: 74AN XY: 74386
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 15 Benign: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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
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not specified Benign:1
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Spastic paraplegia Benign:1
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Hereditary spastic paraplegia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at