chr2-132781095-T-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_207363.3(NCKAP5):c.5006A>T(p.Asn1669Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000282 in 1,613,724 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_207363.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCKAP5 | NM_207363.3 | c.5006A>T | p.Asn1669Ile | missense_variant | 15/20 | ENST00000409261.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCKAP5 | ENST00000409261.6 | c.5006A>T | p.Asn1669Ile | missense_variant | 15/20 | 5 | NM_207363.3 | P1 | |
ENST00000651100.1 | n.458-33506T>A | intron_variant, non_coding_transcript_variant | |||||||
NCKAP5 | ENST00000409213.5 | c.1093-7201A>T | intron_variant | 5 | |||||
NCKAP5 | ENST00000473859.1 | n.219A>T | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00141 AC: 215AN: 152116Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000282 AC: 70AN: 248644Hom.: 0 AF XY: 0.000178 AC XY: 24AN XY: 134894
GnomAD4 exome AF: 0.000164 AC: 240AN: 1461490Hom.: 0 Cov.: 31 AF XY: 0.000153 AC XY: 111AN XY: 726988
GnomAD4 genome ? AF: 0.00141 AC: 215AN: 152234Hom.: 1 Cov.: 33 AF XY: 0.00129 AC XY: 96AN XY: 74414
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at