chr2-70932960-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_012476.3(VAX2):āc.629T>Cā(p.Leu210Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000446 in 1,611,584 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_012476.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VAX2 | NM_012476.3 | c.629T>C | p.Leu210Pro | missense_variant | 3/3 | ENST00000234392.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAX2 | ENST00000234392.3 | c.629T>C | p.Leu210Pro | missense_variant | 3/3 | 1 | NM_012476.3 | P1 | |
VAX2 | ENST00000432367.6 | c.*45+8622T>C | intron_variant, NMD_transcript_variant | 5 | |||||
VAX2 | ENST00000646783.1 | c.80-6458T>C | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00258 AC: 393AN: 152096Hom.: 3 Cov.: 30
GnomAD3 exomes AF: 0.000568 AC: 141AN: 248160Hom.: 0 AF XY: 0.000424 AC XY: 57AN XY: 134454
GnomAD4 exome AF: 0.000223 AC: 326AN: 1459370Hom.: 0 Cov.: 32 AF XY: 0.000193 AC XY: 140AN XY: 725762
GnomAD4 genome AF: 0.00258 AC: 392AN: 152214Hom.: 3 Cov.: 30 AF XY: 0.00250 AC XY: 186AN XY: 74414
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 26, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at