7-100107511-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_139315.3(TAF6):c.1769C>A(p.Thr590Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000476 in 1,614,048 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. T590T) has been classified as Likely benign.
Frequency
Consequence
NM_139315.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAF6 | NM_139315.3 | c.1769C>A | p.Thr590Asn | missense_variant | 15/15 | ENST00000453269.7 | |
AP4M1 | NM_004722.4 | c.*629G>T | 3_prime_UTR_variant | 15/15 | ENST00000359593.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAF6 | ENST00000453269.7 | c.1769C>A | p.Thr590Asn | missense_variant | 15/15 | 1 | NM_139315.3 | P1 | |
AP4M1 | ENST00000359593.9 | c.*629G>T | 3_prime_UTR_variant | 15/15 | 1 | NM_004722.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000876 AC: 22AN: 251076Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135742
GnomAD4 exome AF: 0.000507 AC: 741AN: 1461812Hom.: 1 Cov.: 34 AF XY: 0.000527 AC XY: 383AN XY: 727208
GnomAD4 genome AF: 0.000184 AC: 28AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74380
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2022 | The c.1880C>A (p.T627N) alteration is located in exon 15 (coding exon 15) of the TAF6 gene. This alteration results from a C to A substitution at nucleotide position 1880, causing the threonine (T) at amino acid position 627 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Alazami-Yuan syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Apr 11, 2019 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 29, 2022 | This sequence change replaces threonine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 590 of the TAF6 protein (p.Thr590Asn). This variant is present in population databases (rs138114559, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with TAF6-related conditions. ClinVar contains an entry for this variant (Variation ID: 1030002). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at