rs9302427

Variant names:

• chr16-24704332-C-A
• rs9302427
• NM_001351850.2:c.81-46394C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-24704332-C-A
• chr16-24704332-C-G
• chr16-24704332-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001351850.2(TNRC6A):​c.81-46394C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,728 control chromosomes in the GnomAD database, including 20,694 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 0.50 (20694 hom., cov: 30)
• Consequence: TNRC6A NM_001351850.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560
• Publications: 5 publications found

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]

TNRC6A Gene-Disease associations (from GenCC):

• epilepsy, familial adult myoclonic, 6

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNRC6A	NM_001351850.2	c.81-46394C>A		intron_variant	Intron 2 of 23		NP_001338779.1
TNRC6A	XM_024450231.2	c.81-46394C>A		intron_variant	Intron 2 of 24		XP_024305999.1
TNRC6A	XM_017023144.3	c.81-46394C>A		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.403-46394C>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76080 AN: 151610 Hom.: 20655 Cov.: 30

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.502 AC: 76175 AN: 151728 Hom.: 20694 Cov.: 30 AF XY: 0.508 AC XY: 37652 AN XY: 74130

African (AFR) AF: 0.673 AC: 27838 AN: 41380

American (AMR) AF: 0.520 AC: 7908 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1163 AN: 3464

East Asian (EAS) AF: 0.856 AC: 4407 AN: 5150

South Asian (SAS) AF: 0.491 AC: 2357 AN: 4800

European-Finnish (FIN) AF: 0.455 AC: 4779 AN: 10510

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26430 AN: 67906

Other (OTH) AF: 0.462 AC: 974 AN: 2108

Alfa AF: 0.440 Hom.: 3237

Bravo AF: 0.514

Asia WGS AF: 0.670 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.24
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs9302427; hg19: chr16-24715653;