rs2664537
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000544979.6(ZHX3):c.2747C>T(p.Pro916Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,562,680 control chromosomes in the GnomAD database, including 20,414 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000544979.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZHX3 | NM_001384317.1 | c.*102C>T | 3_prime_UTR_variant | 4/4 | ENST00000683867.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZHX3 | ENST00000683867.1 | c.*102C>T | 3_prime_UTR_variant | 4/4 | NM_001384317.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.139 AC: 21170AN: 152044Hom.: 1709 Cov.: 33
GnomAD3 exomes AF: 0.135 AC: 23557AN: 174830Hom.: 1909 AF XY: 0.130 AC XY: 12037AN XY: 92476
GnomAD4 exome AF: 0.156 AC: 220688AN: 1410518Hom.: 18705 Cov.: 32 AF XY: 0.154 AC XY: 107042AN XY: 696664
GnomAD4 genome ? AF: 0.139 AC: 21180AN: 152162Hom.: 1709 Cov.: 33 AF XY: 0.139 AC XY: 10363AN XY: 74408
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 19, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at