rs58728948
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002518.4(NPAS2):c.2068G>A(p.Ala690Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0018 in 1,614,170 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002518.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPAS2 | NM_002518.4 | c.2068G>A | p.Ala690Thr | missense_variant | 19/21 | ENST00000335681.10 | NP_002509.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPAS2 | ENST00000335681.10 | c.2068G>A | p.Ala690Thr | missense_variant | 19/21 | 1 | NM_002518.4 | ENSP00000338283.5 |
Frequencies
GnomAD3 genomes AF: 0.00907 AC: 1380AN: 152198Hom.: 23 Cov.: 33
GnomAD3 exomes AF: 0.00254 AC: 637AN: 251234Hom.: 6 AF XY: 0.00203 AC XY: 276AN XY: 135834
GnomAD4 exome AF: 0.00104 AC: 1519AN: 1461854Hom.: 18 Cov.: 31 AF XY: 0.000891 AC XY: 648AN XY: 727230
GnomAD4 genome AF: 0.00905 AC: 1379AN: 152316Hom.: 22 Cov.: 33 AF XY: 0.00892 AC XY: 664AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at