16-83972160-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_019065.3(NECAB2):c.211C>T(p.Arg71Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000521 in 1,613,370 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. R71S) 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 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NECAB2 | NM_019065.3 | c.211C>T | p.Arg71Cys | missense_variant | 2/13 | ENST00000305202.9 | |
NECAB2 | NM_001329748.1 | c.211C>T | p.Arg71Cys | missense_variant | 2/12 | ||
NECAB2 | NM_001329749.2 | c.-13C>T | 5_prime_UTR_variant | 2/12 | |||
NECAB2 | XM_047434240.1 | c.-13C>T | 5_prime_UTR_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NECAB2 | ENST00000305202.9 | c.211C>T | p.Arg71Cys | missense_variant | 2/13 | 1 | NM_019065.3 | P1 | |
NECAB2 | ENST00000565691.5 | c.-13C>T | 5_prime_UTR_variant | 1/11 | 1 | ||||
NECAB2 | ENST00000681513.1 | n.616C>T | non_coding_transcript_exon_variant | 2/13 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000640 AC: 16AN: 249832Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135558
GnomAD4 exome AF: 0.0000541 AC: 79AN: 1461138Hom.: 0 Cov.: 31 AF XY: 0.0000578 AC XY: 42AN XY: 726852
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2022 | The c.211C>T (p.R71C) alteration is located in exon 2 (coding exon 2) of the NECAB2 gene. This alteration results from a C to T substitution at nucleotide position 211, causing the arginine (R) at amino acid position 71 to be replaced by a cysteine (C). 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