3-4313393-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006515.4(SETMAR):c.652A>G(p.Ile218Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,613,730 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 Uncertain significance (★).
Frequency
Consequence
NM_006515.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000479 AC: 12AN: 250344Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135336
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1461558Hom.: 0 Cov.: 32 AF XY: 0.0000413 AC XY: 30AN XY: 727082
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.652A>G (p.I218V) alteration is located in exon 2 (coding exon 2) of the SETMAR gene. This alteration results from a A to G substitution at nucleotide position 652, causing the isoleucine (I) at amino acid position 218 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