chr3-47123293-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4_ModerateBS1_SupportingBS2
The NM_014159.7(SETD2):c.1343G>A(p.Arg448Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000264 in 1,551,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. R448R) has been classified as Likely benign.
Frequency
Consequence
NM_014159.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SETD2 | NM_014159.7 | c.1343G>A | p.Arg448Gln | missense_variant | 3/21 | ENST00000409792.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SETD2 | ENST00000409792.4 | c.1343G>A | p.Arg448Gln | missense_variant | 3/21 | 5 | NM_014159.7 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151984Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000631 AC: 10AN: 158556Hom.: 0 AF XY: 0.0000956 AC XY: 8AN XY: 83640
GnomAD4 exome AF: 0.0000279 AC: 39AN: 1399680Hom.: 0 Cov.: 34 AF XY: 0.0000362 AC XY: 25AN XY: 690406
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74360
ClinVar
Submissions by phenotype
Luscan-Lumish syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Jan 07, 2022 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 11, 2018 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at