chr2-132728835-A-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_207363.3(NCKAP5):c.5561T>A(p.Val1854Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000315 in 1,613,802 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_207363.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCKAP5 | NM_207363.3 | c.5561T>A | p.Val1854Asp | missense_variant | 18/20 | ENST00000409261.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCKAP5 | ENST00000409261.6 | c.5561T>A | p.Val1854Asp | missense_variant | 18/20 | 5 | NM_207363.3 | P1 | |
ENST00000651100.1 | n.457+42370A>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00174 AC: 265AN: 152072Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000406 AC: 101AN: 249022Hom.: 0 AF XY: 0.000267 AC XY: 36AN XY: 135082
GnomAD4 exome AF: 0.000168 AC: 245AN: 1461612Hom.: 1 Cov.: 31 AF XY: 0.000154 AC XY: 112AN XY: 727098
GnomAD4 genome AF: 0.00173 AC: 264AN: 152190Hom.: 2 Cov.: 32 AF XY: 0.00176 AC XY: 131AN XY: 74416
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 13, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at