5-55859576-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_139017.7(IL31RA):c.131C>T(p.Ser44Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000691 in 1,612,090 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_139017.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00393 AC: 598AN: 152180Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.000994 AC: 250AN: 251408Hom.: 3 AF XY: 0.000699 AC XY: 95AN XY: 135876
GnomAD4 exome AF: 0.000352 AC: 514AN: 1459792Hom.: 3 Cov.: 31 AF XY: 0.000275 AC XY: 200AN XY: 726190
GnomAD4 genome AF: 0.00394 AC: 600AN: 152298Hom.: 5 Cov.: 32 AF XY: 0.00380 AC XY: 283AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at