16-24643587-C-T

Position:

• chr16-24643587-C-T

Variant summary

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

The NM_001351850.2(TNRC6A):​c.80+2578C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 151,994 control chromosomes in the GnomAD database, including 40,262 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 0.72 (40262 hom., cov: 30)
• Consequence: TNRC6A NM_001351850.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNRC6A	NM_001351850.2	c.80+2578C>T		intron_variant			NP_001338779.1
TNRC6A	XM_017023144.3	c.80+2578C>T		intron_variant			XP_016878633.1
TNRC6A	XM_017023145.3	c.80+2578C>T		intron_variant			XP_016878634.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNRC6A	ENST00000566108.2	n.402+2578C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108938 AN: 151876 Hom.: 40214 Cov.: 30

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.717 AC: 109038 AN: 151994 Hom.: 40262 Cov.: 30 AF XY: 0.714 AC XY: 53027 AN XY: 74290

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.722

Alfa AF: 0.672 Hom.: 68347

Bravo AF: 0.727

Asia WGS AF: 0.639 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.11
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7190684; hg19: chr16-24654908;