21-36036228-T-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_017438.5(SETD4):c.1212A>T(p.Lys404Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00382 in 1,609,066 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_017438.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SETD4 | NM_017438.5 | c.1212A>T | p.Lys404Asn | missense_variant | 11/12 | ENST00000332131.9 | NP_059134.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SETD4 | ENST00000332131.9 | c.1212A>T | p.Lys404Asn | missense_variant | 11/12 | 2 | NM_017438.5 | ENSP00000329189.4 |
Frequencies
GnomAD3 genomes AF: 0.00271 AC: 412AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00296 AC: 726AN: 244864Hom.: 4 AF XY: 0.00315 AC XY: 416AN XY: 132134
GnomAD4 exome AF: 0.00394 AC: 5733AN: 1456734Hom.: 17 Cov.: 31 AF XY: 0.00383 AC XY: 2776AN XY: 724350
GnomAD4 genome AF: 0.00270 AC: 411AN: 152332Hom.: 0 Cov.: 33 AF XY: 0.00256 AC XY: 191AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2022 | SETD4: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at