chr16-24664268-T-C

Variant names:

• chr16-24664268-T-C
• rs8045064
• NM_001351850.2:c.80+23259T>C

Variant summary

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

The NM_001351850.2(TNRC6A):​c.80+23259T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0353 in 151,738 control chromosomes in the GnomAD database, including 144 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 0.035 (144 hom., cov: 31)
• Consequence: TNRC6A NM_001351850.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 10 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]

LINC01567 (HGNC:51367): (long intergenic non-protein coding RNA 1567)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNRC6A	NM_001351850.2	c.80+23259T>C		intron_variant	Intron 2 of 23		NP_001338779.1
LINC01567	NR_122072.1	n.325-264A>G		intron_variant	Intron 2 of 2
TNRC6A	XM_024450231.2	c.80+23259T>C		intron_variant	Intron 2 of 24		XP_024305999.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01567	ENST00000414816.1	n.325-264A>G		intron_variant	Intron 2 of 2	2
TNRC6A	ENST00000566108.2	n.402+23259T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0353 AC: 5350 AN: 151626 Hom.: 144 Cov.: 31

Gnomad AFR AF: 0.00911

Gnomad AMI AF: 0.0232

Gnomad AMR AF: 0.0192

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0613

Gnomad FIN AF: 0.0347

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0558

Gnomad OTH AF: 0.0318

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

GnomAD4 genome AF: 0.0353 AC: 5350 AN: 151738 Hom.: 144 Cov.: 31 AF XY: 0.0344 AC XY: 2549 AN XY: 74130

African (AFR) AF: 0.00908 AC: 376 AN: 41396

American (AMR) AF: 0.0192 AC: 290 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.0343 AC: 119 AN: 3470

East Asian (EAS) AF: 0.00194 AC: 10 AN: 5162

South Asian (SAS) AF: 0.0620 AC: 298 AN: 4804

European-Finnish (FIN) AF: 0.0347 AC: 365 AN: 10514

Middle Eastern (MID) AF: 0.0479 AC: 14 AN: 292

European-Non Finnish (NFE) AF: 0.0558 AC: 3792 AN: 67968

Other (OTH) AF: 0.0310 AC: 65 AN: 2098

Alfa AF: 0.0432 Hom.: 58

Bravo AF: 0.0321

Asia WGS AF: 0.0220 AC: 77 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.50
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs8045064; hg19: chr16-24675589;