16-24718450-C-T

Variant names:

• chr16-24718450-C-T
• rs766181
• NM_001351850.2:c.81-32276C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001351850.2(TNRC6A):​c.81-32276C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,984 control chromosomes in the GnomAD database, including 5,371 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (5371 hom., cov: 31)
• Consequence: TNRC6A NM_001351850.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

Genes affected

TNRC6A (HGNC:11969): (trinucleotide repeat containing adaptor 6A) This gene encodes a member of the trinucleotide repeat containing 6 protein family. The protein functions in post-transcriptional gene silencing through the RNA interference (RNAi) and microRNA pathways. The protein associates with messenger RNAs and Argonaute proteins in cytoplasmic bodies known as GW-bodies or P-bodies. Inhibiting expression of this gene delocalizes other GW-body proteins and impairs RNAi and microRNA-induced gene silencing. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNRC6A	NM_001351850.2	c.81-32276C>T		intron_variant	Intron 2 of 23		NP_001338779.1
TNRC6A	XM_024450231.2	c.81-32276C>T		intron_variant	Intron 2 of 24		XP_024305999.1
TNRC6A	XM_017023144.3	c.81-32276C>T		intron_variant	Intron 2 of 23		XP_016878633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNRC6A	ENST00000566108.2	n.403-32276C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38587 AN: 151866 Hom.: 5370 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.224

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.254 AC: 38598 AN: 151984 Hom.: 5371 Cov.: 31 AF XY: 0.247 AC XY: 18367 AN XY: 74264

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.221

Alfa AF: 0.269 Hom.: 3510

Bravo AF: 0.244

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs766181; hg19: chr16-24729771;