chr15-61854919-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020821.3(VPS13C):c.11112T>A(p.Asn3704Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,160 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020821.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS13C | NM_020821.3 | c.11112T>A | p.Asn3704Lys | missense_variant | 84/85 | ENST00000644861.2 | |
LOC124903501 | XR_007064668.1 | n.159+5447A>T | intron_variant, non_coding_transcript_variant | ||||
VPS13C | NM_017684.5 | c.10983T>A | p.Asn3661Lys | missense_variant | 82/83 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS13C | ENST00000644861.2 | c.11112T>A | p.Asn3704Lys | missense_variant | 84/85 | NM_020821.3 | P3 | ||
ENST00000642740.1 | n.172+5447A>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250454Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135370
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461160Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726892
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.11112T>A (p.N3704K) alteration is located in exon 84 (coding exon 84) of the VPS13C gene. This alteration results from a T to A substitution at nucleotide position 11112, causing the asparagine (N) at amino acid position 3704 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at