2-74416115-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001316764.3(C2orf81):c.145G>A(p.Ala49Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000408 in 1,536,374 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001316764.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C2orf81 | NM_001316764.3 | c.145G>A | p.Ala49Thr | missense_variant | Exon 2 of 3 | ENST00000684111.1 | NP_001303693.1 | |
C2orf81 | NM_001145054.2 | c.154G>A | p.Ala52Thr | missense_variant | Exon 2 of 4 | NP_001138526.1 | ||
C2orf81 | NM_001316766.2 | c.-224G>A | 5_prime_UTR_variant | Exon 2 of 2 | NP_001303695.1 | |||
C2orf81 | NM_001316765.2 | c.102+43G>A | intron_variant | Intron 2 of 2 | NP_001303694.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C2orf81 | ENST00000684111.1 | c.145G>A | p.Ala49Thr | missense_variant | Exon 2 of 3 | NM_001316764.3 | ENSP00000507340.1 | |||
ENSG00000159239 | ENST00000517883.2 | n.-224G>A | non_coding_transcript_exon_variant | Exon 2 of 5 | 5 | ENSP00000431103.2 | ||||
ENSG00000159239 | ENST00000517883.2 | n.-224G>A | 5_prime_UTR_variant | Exon 2 of 5 | 5 | ENSP00000431103.2 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152256Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000205 AC: 32AN: 155780Hom.: 0 AF XY: 0.000218 AC XY: 18AN XY: 82656
GnomAD4 exome AF: 0.000430 AC: 595AN: 1384118Hom.: 0 Cov.: 32 AF XY: 0.000378 AC XY: 258AN XY: 682432
GnomAD4 genome AF: 0.000210 AC: 32AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.154G>A (p.A52T) alteration is located in exon 2 (coding exon 2) of the C2orf81 gene. This alteration results from a G to A substitution at nucleotide position 154, causing the alanine (A) at amino acid position 52 to be replaced by a threonine (T). 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