rs200484
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003519.4(H2BC13):āc.11T>Cā(p.Leu4Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 1,613,976 control chromosomes in the GnomAD database, including 12,384 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003519.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
H2BC13 | NM_003519.4 | c.11T>C | p.Leu4Pro | missense_variant | 1/1 | ENST00000377401.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
H2BC13 | ENST00000377401.4 | c.11T>C | p.Leu4Pro | missense_variant | 1/1 | NM_003519.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.123 AC: 18631AN: 152020Hom.: 1306 Cov.: 32
GnomAD3 exomes AF: 0.0983 AC: 24697AN: 251350Hom.: 1452 AF XY: 0.0951 AC XY: 12913AN XY: 135848
GnomAD4 exome AF: 0.118 AC: 172086AN: 1461838Hom.: 11077 Cov.: 32 AF XY: 0.115 AC XY: 83460AN XY: 727220
GnomAD4 genome ? AF: 0.123 AC: 18643AN: 152138Hom.: 1307 Cov.: 32 AF XY: 0.118 AC XY: 8764AN XY: 74414
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at