10-100487755-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015490.4(SEC31B):c.3401G>A(p.Arg1134Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,614,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015490.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250720Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135558
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461696Hom.: 0 Cov.: 34 AF XY: 0.0000151 AC XY: 11AN XY: 727136
GnomAD4 genome AF: 0.000118 AC: 18AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3401G>A (p.R1134Q) alteration is located in exon 26 (coding exon 25) of the SEC31B gene. This alteration results from a G to A substitution at nucleotide position 3401, causing the arginine (R) at amino acid position 1134 to be replaced by a glutamine (Q). 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