chr4-372807-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003441.4(ZNF141):āc.370A>Gā(p.Lys124Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00548 in 1,613,866 control chromosomes in the GnomAD database, including 413 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003441.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF141 | NM_003441.4 | c.370A>G | p.Lys124Glu | missense_variant | 4/4 | ENST00000240499.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF141 | ENST00000240499.8 | c.370A>G | p.Lys124Glu | missense_variant | 4/4 | 1 | NM_003441.4 | P1 | |
ZNF141 | ENST00000512994.5 | c.370A>G | p.Lys124Glu | missense_variant | 4/5 | 1 | |||
ZNF141 | ENST00000505939.5 | c.227-10288A>G | intron_variant | 5 | |||||
ZNF141 | ENST00000366506.4 | n.317A>G | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0284 AC: 4317AN: 152200Hom.: 202 Cov.: 33
GnomAD3 exomes AF: 0.00763 AC: 1915AN: 250924Hom.: 86 AF XY: 0.00562 AC XY: 763AN XY: 135676
GnomAD4 exome AF: 0.00309 AC: 4517AN: 1461548Hom.: 211 Cov.: 31 AF XY: 0.00269 AC XY: 1955AN XY: 727068
GnomAD4 genome AF: 0.0284 AC: 4332AN: 152318Hom.: 202 Cov.: 33 AF XY: 0.0268 AC XY: 1996AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at