rs201439692
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_012082.4(ZFPM2):c.1227G>T(p.Gln409His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000171 in 1,613,910 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q409R) has been classified as Uncertain significance.
Frequency
Consequence
NM_012082.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFPM2 | NM_012082.4 | c.1227G>T | p.Gln409His | missense_variant | 8/8 | ENST00000407775.7 | |
ZFPM2-AS1 | NR_125797.1 | n.191-2867C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFPM2 | ENST00000407775.7 | c.1227G>T | p.Gln409His | missense_variant | 8/8 | 1 | NM_012082.4 | P1 | |
ZFPM2-AS1 | ENST00000520433.5 | n.212-2867C>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000887 AC: 135AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000261 AC: 65AN: 248988Hom.: 0 AF XY: 0.000170 AC XY: 23AN XY: 135068
GnomAD4 exome AF: 0.0000965 AC: 141AN: 1461676Hom.: 0 Cov.: 31 AF XY: 0.0000729 AC XY: 53AN XY: 727124
GnomAD4 genome ? AF: 0.000887 AC: 135AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.000820 AC XY: 61AN XY: 74414
ClinVar
Submissions by phenotype
46,XY sex reversal 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 02, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at