16-83972160-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001329749.2(NECAB2):c.-13C>T variant causes a 5 prime UTR premature start codon gain 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 (★).
Frequency
Consequence
NM_001329749.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NECAB2 | ENST00000565691 | c.-13C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 11 | 1 | ENSP00000457354.1 | ||||
NECAB2 | ENST00000305202.9 | c.211C>T | p.Arg71Cys | missense_variant | Exon 2 of 13 | 1 | NM_019065.3 | ENSP00000307449.4 | ||
NECAB2 | ENST00000565691 | c.-13C>T | 5_prime_UTR_variant | Exon 1 of 11 | 1 | ENSP00000457354.1 | ||||
NECAB2 | ENST00000681513.1 | n.616C>T | non_coding_transcript_exon_variant | Exon 2 of 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
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