chr1-35370408-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005095.3(ZMYM4):c.962C>T(p.Ala321Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000398 in 1,505,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005095.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZMYM4 | ENST00000314607.11 | c.962C>T | p.Ala321Val | missense_variant | Exon 7 of 30 | 2 | NM_005095.3 | ENSP00000322915.6 | ||
ZMYM4 | ENST00000457946.1 | c.206C>T | p.Ala69Val | missense_variant | Exon 3 of 24 | 5 | ENSP00000400506.1 | |||
ZMYM4 | ENST00000482131.1 | n.195C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000799 AC: 1AN: 125220Hom.: 0 Cov.: 27
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248002Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134454
GnomAD4 exome AF: 0.00000362 AC: 5AN: 1380534Hom.: 0 Cov.: 39 AF XY: 0.00000437 AC XY: 3AN XY: 687244
GnomAD4 genome AF: 0.00000798 AC: 1AN: 125268Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 58586
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.962C>T (p.A321V) alteration is located in exon 7 (coding exon 7) of the ZMYM4 gene. This alteration results from a C to T substitution at nucleotide position 962, causing the alanine (A) at amino acid position 321 to be replaced by a valine (V). 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