1-12847790-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001013631.3(HNRNPCL1):c.500G>A(p.Arg167Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000187 in 1,606,328 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R167P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001013631.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000667 AC: 10AN: 149978Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248906Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135000
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1456350Hom.: 2 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 724488
GnomAD4 genome AF: 0.0000667 AC: 10AN: 149978Hom.: 0 Cov.: 30 AF XY: 0.0000821 AC XY: 6AN XY: 73092
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.500G>A (p.R167Q) alteration is located in exon 2 (coding exon 1) of the HNRNPCL1 gene. This alteration results from a G to A substitution at nucleotide position 500, causing the arginine (R) at amino acid position 167 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