1-203797823-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001395895.1(ZBED6):c.301T>G(p.Leu101Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,535,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001395895.1 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 |
---|---|---|---|---|---|---|---|
ZBED6 | NM_001395895.1 | c.301T>G | p.Leu101Val | missense_variant | 1/17 | ENST00000550078.3 | |
ZC3H11A | NM_001376342.1 | c.-1588+2029T>G | intron_variant | ENST00000367210.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBED6 | ENST00000550078.3 | c.301T>G | p.Leu101Val | missense_variant | 1/17 | 1 | NM_001395895.1 | P1 | |
ZC3H11A | ENST00000367210.3 | c.-1588+2029T>G | intron_variant | 1 | NM_001376342.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000372 AC: 5AN: 134304Hom.: 0 AF XY: 0.0000547 AC XY: 4AN XY: 73148
GnomAD4 exome AF: 0.0000412 AC: 57AN: 1383794Hom.: 0 Cov.: 33 AF XY: 0.0000366 AC XY: 25AN XY: 682840
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.301T>G (p.L101V) alteration is located in exon 1 (coding exon 1) of the ZBED6 gene. This alteration results from a T to G substitution at nucleotide position 301, causing the leucine (L) at amino acid position 101 to be replaced by a valine (V). 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