chr16-72787494-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006885.4(ZFHX3):c.10782C>G(p.Asn3594Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,476 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_006885.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFHX3 | NM_006885.4 | c.10782C>G | p.Asn3594Lys | missense_variant | 10/10 | ENST00000268489.10 | |
ZFHX3-AS1 | NR_171702.1 | n.391-33279G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFHX3 | ENST00000268489.10 | c.10782C>G | p.Asn3594Lys | missense_variant | 10/10 | 1 | NM_006885.4 | P1 | |
ZFHX3-AS1 | ENST00000687589.1 | n.482+5675G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 151990Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 250982Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135676
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461486Hom.: 0 Cov.: 36 AF XY: 0.0000193 AC XY: 14AN XY: 726970
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 151990Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74210
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2023 | The c.10782C>G (p.N3594K) alteration is located in exon 10 (coding exon 9) of the ZFHX3 gene. This alteration results from a C to G substitution at nucleotide position 10782, causing the asparagine (N) at amino acid position 3594 to be replaced by a lysine (K). 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