chr1-224305156-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002533.4(NVL):āc.626A>Cā(p.Asp209Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000337 in 1,452,762 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 (ā ).
Frequency
Consequence
NM_002533.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NVL | NM_002533.4 | c.626A>C | p.Asp209Ala | missense_variant | 7/23 | ENST00000281701.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NVL | ENST00000281701.11 | c.626A>C | p.Asp209Ala | missense_variant | 7/23 | 1 | NM_002533.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000827 AC: 2AN: 241814Hom.: 0 AF XY: 0.00000766 AC XY: 1AN XY: 130538
GnomAD4 exome AF: 0.0000337 AC: 49AN: 1452762Hom.: 0 Cov.: 32 AF XY: 0.0000346 AC XY: 25AN XY: 722328
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2022 | The c.626A>C (p.D209A) alteration is located in exon 7 (coding exon 7) of the NVL gene. This alteration results from a A to C substitution at nucleotide position 626, causing the aspartic acid (D) at amino acid position 209 to be replaced by an alanine (A). 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