chr16-24789303-T-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014494.4(TNRC6A):c.661T>A(p.Ser221Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,614,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014494.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNRC6A | NM_014494.4 | c.661T>A | p.Ser221Thr | missense_variant | 6/25 | ENST00000395799.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNRC6A | ENST00000395799.8 | c.661T>A | p.Ser221Thr | missense_variant | 6/25 | 5 | NM_014494.4 | A2 | |
TNRC6A | ENST00000491718.5 | c.*186T>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/22 | 1 | ||||
TNRC6A | ENST00000315183.11 | c.661T>A | p.Ser221Thr | missense_variant | 6/24 | 5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250242Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135718
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461846Hom.: 0 Cov.: 30 AF XY: 0.0000344 AC XY: 25AN XY: 727216
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2023 | The c.661T>A (p.S221T) alteration is located in exon 6 (coding exon 6) of the TNRC6A gene. This alteration results from a T to A substitution at nucleotide position 661, causing the serine (S) at amino acid position 221 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at