19-51965074-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_021632.4(ZNF350):c.1379C>T(p.Ala460Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000709 in 1,614,114 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_021632.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF350 | NM_021632.4 | c.1379C>T | p.Ala460Val | missense_variant | 5/5 | ENST00000243644.9 | |
ZNF350-AS1 | NR_103847.1 | n.103-11317G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF350 | ENST00000243644.9 | c.1379C>T | p.Ala460Val | missense_variant | 5/5 | 1 | NM_021632.4 | P1 | |
ZNF350-AS1 | ENST00000595010.4 | n.121-11317G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00356 AC: 541AN: 152136Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00107 AC: 269AN: 251280Hom.: 1 AF XY: 0.000832 AC XY: 113AN XY: 135792
GnomAD4 exome AF: 0.000413 AC: 604AN: 1461860Hom.: 4 Cov.: 34 AF XY: 0.000389 AC XY: 283AN XY: 727232
GnomAD4 genome AF: 0.00355 AC: 541AN: 152254Hom.: 3 Cov.: 32 AF XY: 0.00356 AC XY: 265AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at