2-100964090-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_002518.4(NPAS2):āc.631A>Gā(p.Thr211Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000861 in 1,613,794 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T211I) has been classified as Uncertain significance.
Frequency
Consequence
NM_002518.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPAS2 | NM_002518.4 | c.631A>G | p.Thr211Ala | missense_variant | 8/21 | ENST00000335681.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPAS2 | ENST00000335681.10 | c.631A>G | p.Thr211Ala | missense_variant | 8/21 | 1 | NM_002518.4 | P1 | |
NPAS2 | ENST00000448812.5 | c.567-4191A>G | intron_variant | 5 | |||||
NPAS2 | ENST00000486017.5 | n.678A>G | non_coding_transcript_exon_variant | 7/7 | 3 | ||||
NPAS2 | ENST00000492373.1 | n.408A>G | non_coding_transcript_exon_variant | 5/6 | 4 |
Frequencies
GnomAD3 genomes AF: 0.000481 AC: 73AN: 151892Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000433 AC: 109AN: 251446Hom.: 0 AF XY: 0.000464 AC XY: 63AN XY: 135894
GnomAD4 exome AF: 0.000901 AC: 1317AN: 1461784Hom.: 1 Cov.: 30 AF XY: 0.000862 AC XY: 627AN XY: 727200
GnomAD4 genome AF: 0.000480 AC: 73AN: 152010Hom.: 0 Cov.: 33 AF XY: 0.000350 AC XY: 26AN XY: 74314
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at