chr16-24789312-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014494.4(TNRC6A):c.670A>G(p.Asn224Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000178 in 1,614,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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.670A>G | p.Asn224Asp | missense_variant | 6/25 | ENST00000395799.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNRC6A | ENST00000395799.8 | c.670A>G | p.Asn224Asp | missense_variant | 6/25 | 5 | NM_014494.4 | A2 | |
TNRC6A | ENST00000491718.5 | c.*195A>G | 3_prime_UTR_variant, NMD_transcript_variant | 3/22 | 1 | ||||
TNRC6A | ENST00000315183.11 | c.670A>G | p.Asn224Asp | missense_variant | 6/24 | 5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000160 AC: 40AN: 250306Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135744
GnomAD4 exome AF: 0.000181 AC: 264AN: 1461874Hom.: 0 Cov.: 30 AF XY: 0.000184 AC XY: 134AN XY: 727234
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2022 | The c.670A>G (p.N224D) alteration is located in exon 6 (coding exon 6) of the TNRC6A gene. This alteration results from a A to G substitution at nucleotide position 670, causing the asparagine (N) at amino acid position 224 to be replaced by an aspartic acid (D). 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