chr9-21305072-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_002169.3(IFNA5):c.185C>T(p.Pro62Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000979 in 1,614,224 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002169.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNA5 | NM_002169.3 | c.185C>T | p.Pro62Leu | missense_variant | 1/1 | ENST00000610521.2 | |
LOC107987053 | XR_001746634.2 | n.472-31549G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNA5 | ENST00000610521.2 | c.185C>T | p.Pro62Leu | missense_variant | 1/1 | NM_002169.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152212Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000199 AC: 50AN: 251466Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135910
GnomAD4 exome AF: 0.0000862 AC: 126AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.0000894 AC XY: 65AN XY: 727248
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152330Hom.: 1 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74492
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 22, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at