rs8045064

chr16-24664268-T-C

Variant summary

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

The NR_122072.1(LINC01567):n.325-264A>G variant causes a intron, non coding transcript 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: LINC01567 NR_122072.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

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

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=-0.92).
• 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/exons	MANE	UniProt
LINC01567	NR_122072.1	n.325-264A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01567	ENST00000414816.1	n.325-264A>G		intron_variant, non_coding_transcript_variant		2
TNRC6A	ENST00000566108.2	n.402+23259T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.00908

Gnomad4 AMR AF: 0.0192

Gnomad4 ASJ AF: 0.0343

Gnomad4 EAS AF: 0.00194

Gnomad4 SAS AF: 0.0620

Gnomad4 FIN AF: 0.0347

Gnomad4 NFE AF: 0.0558

Gnomad4 OTH AF: 0.0310

Alfa AF: 0.0462 Hom.: 29

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8045064; hg19: chr16-24675589;