chr16-83972160-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_019065.3(NECAB2):c.211C>A(p.Arg71Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,492 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R71C) has been classified as Uncertain significance.
Frequency
Consequence
NM_019065.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NECAB2 | NM_019065.3 | c.211C>A | p.Arg71Ser | missense_variant | 2/13 | ENST00000305202.9 | |
NECAB2 | NM_001329748.1 | c.211C>A | p.Arg71Ser | missense_variant | 2/12 | ||
NECAB2 | NM_001329749.2 | c.-13C>A | 5_prime_UTR_variant | 2/12 | |||
NECAB2 | XM_047434240.1 | c.-13C>A | 5_prime_UTR_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NECAB2 | ENST00000305202.9 | c.211C>A | p.Arg71Ser | missense_variant | 2/13 | 1 | NM_019065.3 | P1 | |
NECAB2 | ENST00000565691.5 | c.-13C>A | 5_prime_UTR_variant | 1/11 | 1 | ||||
NECAB2 | ENST00000681513.1 | n.616C>A | non_coding_transcript_exon_variant | 2/13 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461144Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726856
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2024 | The c.211C>A (p.R71S) alteration is located in exon 2 (coding exon 2) of the NECAB2 gene. This alteration results from a C to A substitution at nucleotide position 211, causing the arginine (R) at amino acid position 71 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.