3-136946128-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001291999.2(NCK1):āc.772G>Cā(p.Gly258Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00358 in 1,613,712 control chromosomes in the GnomAD database, including 171 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_001291999.2 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 |
---|---|---|---|---|---|---|---|
NCK1 | NM_001291999.2 | c.772G>C | p.Gly258Arg | missense_variant | 3/4 | ENST00000481752.6 | |
IL20RB-AS1 | NR_183727.1 | n.621C>G | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCK1 | ENST00000481752.6 | c.772G>C | p.Gly258Arg | missense_variant | 3/4 | 5 | NM_001291999.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0194 AC: 2937AN: 151728Hom.: 76 Cov.: 31
GnomAD3 exomes AF: 0.00525 AC: 1321AN: 251408Hom.: 42 AF XY: 0.00373 AC XY: 507AN XY: 135872
GnomAD4 exome AF: 0.00194 AC: 2832AN: 1461866Hom.: 95 Cov.: 31 AF XY: 0.00169 AC XY: 1228AN XY: 727230
GnomAD4 genome AF: 0.0194 AC: 2940AN: 151846Hom.: 76 Cov.: 31 AF XY: 0.0185 AC XY: 1373AN XY: 74222
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 04, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at