chr16-88528136-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153813.3(ZFPM1):āc.610A>Gā(p.Lys204Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000487 in 1,600,794 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_153813.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFPM1 | NM_153813.3 | c.610A>G | p.Lys204Glu | missense_variant | 6/10 | ENST00000319555.8 | |
ZFPM1-AS1 | NR_148997.1 | n.289+2306T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFPM1 | ENST00000319555.8 | c.610A>G | p.Lys204Glu | missense_variant | 6/10 | 1 | NM_153813.3 | P1 | |
ZFPM1-AS1 | ENST00000563243.1 | n.289+2306T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000662 AC: 1AN: 151102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000131 AC: 3AN: 229732Hom.: 0 AF XY: 0.00000799 AC XY: 1AN XY: 125234
GnomAD4 exome AF: 0.0000531 AC: 77AN: 1449692Hom.: 0 Cov.: 31 AF XY: 0.0000541 AC XY: 39AN XY: 720284
GnomAD4 genome AF: 0.00000662 AC: 1AN: 151102Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73790
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.610A>G (p.K204E) alteration is located in exon 6 (coding exon 6) of the ZFPM1 gene. This alteration results from a A to G substitution at nucleotide position 610, causing the lysine (K) at amino acid position 204 to be replaced by a glutamic acid (E). 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