4-40102431-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_018177.6(N4BP2):āc.586A>Gā(p.Met196Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00546 in 1,612,076 control chromosomes in the GnomAD database, including 432 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_018177.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
N4BP2 | NM_018177.6 | c.586A>G | p.Met196Val | missense_variant | 4/18 | ENST00000261435.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
N4BP2 | ENST00000261435.11 | c.586A>G | p.Met196Val | missense_variant | 4/18 | 5 | NM_018177.6 | P1 | |
N4BP2 | ENST00000511480.5 | c.*377A>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/19 | 1 | ||||
N4BP2 | ENST00000515550.1 | c.346A>G | p.Met116Val | missense_variant | 3/3 | 3 | |||
N4BP2 | ENST00000706658.1 | c.*377A>G | 3_prime_UTR_variant, NMD_transcript_variant | 7/21 |
Frequencies
GnomAD3 genomes AF: 0.0286 AC: 4352AN: 152166Hom.: 224 Cov.: 32
GnomAD3 exomes AF: 0.00766 AC: 1901AN: 248236Hom.: 96 AF XY: 0.00594 AC XY: 800AN XY: 134656
GnomAD4 exome AF: 0.00303 AC: 4430AN: 1459792Hom.: 206 Cov.: 33 AF XY: 0.00268 AC XY: 1949AN XY: 726220
GnomAD4 genome AF: 0.0287 AC: 4372AN: 152284Hom.: 226 Cov.: 32 AF XY: 0.0280 AC XY: 2084AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 08, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at