chr20-1455004-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016143.5(NSFL1C):c.407G>A(p.Arg136Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,614,056 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016143.5 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: 0.0000920 AC: 14AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000207 AC: 52AN: 251436Hom.: 0 AF XY: 0.000280 AC XY: 38AN XY: 135892
GnomAD4 exome AF: 0.000105 AC: 154AN: 1461746Hom.: 1 Cov.: 31 AF XY: 0.000153 AC XY: 111AN XY: 727186
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152310Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.413G>A (p.R138Q) alteration is located in exon 5 (coding exon 5) of the NSFL1C gene. This alteration results from a G to A substitution at nucleotide position 413, causing the arginine (R) at amino acid position 138 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