19-52155579-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001102657.3(ZNF836):c.2104G>A(p.Ala702Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,613,950 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001102657.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF836 | NM_001102657.3 | c.2104G>A | p.Ala702Thr | missense_variant | Exon 5 of 5 | ENST00000682614.1 | NP_001096127.1 | |
ZNF836 | XM_011526558.4 | c.2104G>A | p.Ala702Thr | missense_variant | Exon 5 of 5 | XP_011524860.1 | ||
ZNF836 | XM_011526559.4 | c.2104G>A | p.Ala702Thr | missense_variant | Exon 4 of 4 | XP_011524861.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF836 | ENST00000682614.1 | c.2104G>A | p.Ala702Thr | missense_variant | Exon 5 of 5 | NM_001102657.3 | ENSP00000507838.1 | |||
ZNF836 | ENST00000597252.5 | c.2104G>A | p.Ala702Thr | missense_variant | Exon 5 of 5 | 2 | ENSP00000470239.1 | |||
ENSG00000267827 | ENST00000594362.1 | n.554+4886G>A | intron_variant | Intron 4 of 4 | 5 | |||||
ENSG00000267827 | ENST00000598982.5 | n.494+4886G>A | intron_variant | Intron 4 of 4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000721 AC: 18AN: 249696Hom.: 2 AF XY: 0.000111 AC XY: 15AN XY: 135454
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461694Hom.: 2 Cov.: 34 AF XY: 0.0000536 AC XY: 39AN XY: 727124
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74436
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2104G>A (p.A702T) alteration is located in exon 5 (coding exon 3) of the ZNF836 gene. This alteration results from a G to A substitution at nucleotide position 2104, causing the alanine (A) at amino acid position 702 to be replaced by a threonine (T). 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