3-4313663-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006515.4(SETMAR):c.922G>A(p.Val308Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0001 in 1,613,960 control chromosomes in the GnomAD database, including 1 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_006515.4 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 |
---|---|---|---|---|---|---|---|
SETMAR | NM_006515.4 | c.922G>A | p.Val308Ile | missense_variant | 2/3 | ENST00000358065.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SETMAR | ENST00000358065.5 | c.922G>A | p.Val308Ile | missense_variant | 2/3 | 1 | NM_006515.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000152 AC: 38AN: 250180Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135318
GnomAD4 exome AF: 0.0000910 AC: 133AN: 1461698Hom.: 1 Cov.: 33 AF XY: 0.0000949 AC XY: 69AN XY: 727152
GnomAD4 genome ? AF: 0.000190 AC: 29AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.922G>A (p.V308I) alteration is located in exon 2 (coding exon 2) of the SETMAR gene. This alteration results from a G to A substitution at nucleotide position 922, causing the valine (V) at amino acid position 308 to be replaced by an isoleucine (I). 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