chr1-112724067-A-C
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP3BP6_Moderate
The NM_182759.3(TAFA3):āc.320A>Cā(p.Glu107Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,302 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000020 ( 0 hom., cov: 31)
Exomes š: 0.000021 ( 0 hom. )
Consequence
TAFA3
NM_182759.3 missense
NM_182759.3 missense
Scores
11
3
3
Clinical Significance
Conservation
PhyloP100: 9.32
Genes affected
TAFA3 (HGNC:21590): (TAFA chemokine like family member 3) This gene is a member of the TAFA family which is composed of five highly homologous genes that encode small secreted proteins. These proteins contain conserved cysteine residues at fixed positions, and are distantly related to MIP-1alpha, a member of the CC-chemokine family. The TAFA proteins are predominantly expressed in specific regions of the brain, and are postulated to function as brain-specific chemokines or neurokines, that act as regulators of immune and nervous cells. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.834
BP6
Variant 1-112724067-A-C is Benign according to our data. Variant chr1-112724067-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 3173611.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAFA3 | NM_182759.3 | c.320A>C | p.Glu107Ala | missense_variant | 5/6 | ENST00000361886.4 | |
TAFA3 | NM_001004440.2 | c.388A>C | p.Arg130= | synonymous_variant | 5/6 | ||
TAFA3 | NR_169586.1 | n.811A>C | non_coding_transcript_exon_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAFA3 | ENST00000361886.4 | c.320A>C | p.Glu107Ala | missense_variant | 5/6 | 1 | NM_182759.3 | P1 | |
TAFA3 | ENST00000369630.7 | c.388A>C | p.Arg130= | synonymous_variant | 4/5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151842Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250948Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135706
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GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461460Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727048
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GnomAD4 genome AF: 0.0000198 AC: 3AN: 151842Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74182
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | 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
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D
M_CAP
Benign
T
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D
PROVEAN
Pathogenic
D
REVEL
Pathogenic
Sift
Pathogenic
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
ClinPred
D
GERP RS
Varity_R
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at