chr3-159995456-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000882.4(IL12A):c.659C>T(p.Pro220Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000718 in 1,607,448 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P220P) has been classified as Benign.
Frequency
Consequence
NM_000882.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL12A | NM_001397992.1 | c.557C>T | p.Pro186Leu | missense_variant | 7/7 | ENST00000699704.1 | |
IL12A | NM_000882.4 | c.659C>T | p.Pro220Leu | missense_variant | 7/7 | ||
IL12A-AS1 | NR_108088.1 | n.1085-1151G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL12A | ENST00000699704.1 | c.557C>T | p.Pro186Leu | missense_variant | 7/7 | NM_001397992.1 | P1 | ||
IL12A-AS1 | ENST00000497452.5 | n.1085-1151G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000519 AC: 79AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000761 AC: 187AN: 245812Hom.: 1 AF XY: 0.000715 AC XY: 95AN XY: 132912
GnomAD4 exome AF: 0.000739 AC: 1075AN: 1455144Hom.: 2 Cov.: 29 AF XY: 0.000716 AC XY: 518AN XY: 723836
GnomAD4 genome AF: 0.000519 AC: 79AN: 152304Hom.: 0 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 22, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at