chr4-25418176-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_013367.3(ANAPC4):c.2221G>T(p.Val741Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013367.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANAPC4 | NM_013367.3 | c.2221G>T | p.Val741Leu | missense_variant | 29/29 | ENST00000315368.8 | |
ANAPC4 | NM_001286756.2 | c.2224G>T | p.Val742Leu | missense_variant | 29/29 | ||
ANAPC4 | XM_011513838.2 | c.1888G>T | p.Val630Leu | missense_variant | 27/27 | ||
ANAPC4 | XM_005248159.2 | c.1120G>T | p.Val374Leu | missense_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANAPC4 | ENST00000315368.8 | c.2221G>T | p.Val741Leu | missense_variant | 29/29 | 1 | NM_013367.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250440Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135380
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461552Hom.: 0 Cov.: 30 AF XY: 0.0000303 AC XY: 22AN XY: 727042
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.2221G>T (p.V741L) alteration is located in exon 29 (coding exon 28) of the ANAPC4 gene. This alteration results from a G to T substitution at nucleotide position 2221, causing the valine (V) at amino acid position 741 to be replaced by a leucine (L). 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