12-71619960-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4BS2_Supporting
The NM_144982.5(ZFC3H1):āc.5015T>Cā(p.Val1672Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000138 in 1,597,550 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 (ā ).
Frequency
Consequence
NM_144982.5 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 |
---|---|---|---|---|---|---|---|
ZFC3H1 | NM_144982.5 | c.5015T>C | p.Val1672Ala | missense_variant | 26/35 | ENST00000378743.9 | |
ZFC3H1 | XM_047428485.1 | c.3836T>C | p.Val1279Ala | missense_variant | 26/35 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFC3H1 | ENST00000378743.9 | c.5015T>C | p.Val1672Ala | missense_variant | 26/35 | 1 | NM_144982.5 | P1 | |
ZFC3H1 | ENST00000552994.5 | c.5015T>C | p.Val1672Ala | missense_variant, NMD_transcript_variant | 26/34 | 1 | |||
ZFC3H1 | ENST00000546771.1 | n.6T>C | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151996Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243154Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131760
GnomAD4 exome AF: 0.0000145 AC: 21AN: 1445554Hom.: 0 Cov.: 30 AF XY: 0.0000126 AC XY: 9AN XY: 716370
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151996Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74246
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.5015T>C (p.V1672A) alteration is located in exon 26 (coding exon 26) of the ZFC3H1 gene. This alteration results from a T to C substitution at nucleotide position 5015, causing the valine (V) at amino acid position 1672 to be replaced by an alanine (A). 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