16-24777101-AGCAGCCACAGCC-A

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_014494.4(TNRC6A):c.339_350del(p.Pro115_Gln118del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,804 control chromosomes in the GnomAD database, including 1,900 homozygotes. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.15 (1900 hom., cov: 29)
  • Exomes 𝑓: 0.18 (24888 hom.)
  • Failed GnomAD Quality Control
• Consequence: TNRC6A NM_014494.4 inframe_deletion
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 3.07

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 -16 ACMG points.

• BP6: Variant 16-24777101-AGCAGCCACAGCC-A is Benign according to our data. Variant chr16-24777101-AGCAGCCACAGCC-A is described in ClinVar as [Benign]. Clinvar id is 769896.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNRC6A	NM_014494.4	c.339_350del	p.Pro115_Gln118del	inframe_deletion	5/25	ENST00000395799.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNRC6A	ENST00000395799.8	c.339_350del	p.Pro115_Gln118del	inframe_deletion	5/25	5	NM_014494.4	A2
TNRC6A	ENST00000315183.11	c.339_350del	p.Pro115_Gln118del	inframe_deletion	5/24	5		P4

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23284 AN: 151684 Hom.: 1901 Cov.: 29

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.177

GnomAD3 exomes AF: 0.159 AC: 39120 AN: 245404 Hom.: 3284 AF XY: 0.162 AC XY: 21637 AN XY: 133762

Gnomad AFR exome AF: 0.0907

Gnomad AMR exome AF: 0.159

Gnomad ASJ exome AF: 0.154

Gnomad EAS exome AF: 0.101

Gnomad SAS exome AF: 0.148

Gnomad FIN exome AF: 0.133

Gnomad NFE exome AF: 0.186

Gnomad OTH exome AF: 0.165

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.180 AC: 262766 AN: 1458362 Hom.: 24888 AF XY: 0.179 AC XY: 130110 AN XY: 725568

Gnomad4 AFR exome AF: 0.0954

Gnomad4 AMR exome AF: 0.158

Gnomad4 ASJ exome AF: 0.151

Gnomad4 EAS exome AF: 0.0934

Gnomad4 SAS exome AF: 0.151

Gnomad4 FIN exome AF: 0.133

Gnomad4 NFE exome AF: 0.192

Gnomad4 OTH exome AF: 0.174

GnomAD4 genome AF: 0.153 AC: 23270 AN: 151804 Hom.: 1900 Cov.: 29 AF XY: 0.148 AC XY: 10991 AN XY: 74210

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.175

Alfa AF: 0.00108 Hom.: 0

Asia WGS AF: 0.120 AC: 418 AN: 3466

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Epilepsy, familial adult myoclonic, 6 Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71156436; hg19: chr16-24788422;