3-183806882-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_018023.5(YEATS2):c.3801C>A(p.Phe1267Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018023.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
YEATS2 | ENST00000305135.10 | c.3801C>A | p.Phe1267Leu | missense_variant | Exon 28 of 31 | 1 | NM_018023.5 | ENSP00000306983.5 | ||
YEATS2-AS1 | ENST00000425008.3 | n.2017G>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 4 | |||||
YEATS2 | ENST00000472593.1 | n.3229C>A | non_coding_transcript_exon_variant | Exon 2 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249418Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135336
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461672Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727146
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3801C>A (p.F1267L) alteration is located in exon 28 (coding exon 27) of the YEATS2 gene. This alteration results from a C to A substitution at nucleotide position 3801, causing the phenylalanine (F) at amino acid position 1267 to be replaced by a leucine (L). 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