chr6-75640695-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015571.4(SENP6):c.470G>A(p.Arg157Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000159 in 1,512,406 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_015571.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SENP6 | NM_015571.4 | c.470G>A | p.Arg157Gln | missense_variant | 6/24 | ENST00000447266.7 | |
SENP6 | NM_001100409.3 | c.458+5884G>A | intron_variant | ||||
SENP6 | NM_001304792.2 | c.458+5884G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SENP6 | ENST00000447266.7 | c.470G>A | p.Arg157Gln | missense_variant | 6/24 | 1 | NM_015571.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151798Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000162 AC: 22AN: 1360608Hom.: 0 Cov.: 24 AF XY: 0.00000740 AC XY: 5AN XY: 675572
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151798Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74118
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at