rs139911

chr22-40308048-C-T

Variant summary

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

The NM_001162501.2(TNRC6B):c.4121-464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,064 control chromosomes in the GnomAD database, including 35,776 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 0.67 (35776 hom., cov: 31)
• Consequence: TNRC6B NM_001162501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

Genes affected

TNRC6B (HGNC:29190): (trinucleotide repeat containing adaptor 6B) Enables RNA binding activity. Involved in regulation of gene expression. Predicted to be located in cytosol. Predicted to be active in P-body and nucleoplasm. Implicated in subserous uterine fibroid and uterine fibroid. [provided by Alliance of Genome Resources, Apr 2022]

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 (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNRC6B	NM_001162501.2	c.4121-464C>T		intron_variant		ENST00000454349.7
TNRC6B	NM_001024843.2	c.1709-464C>T		intron_variant
TNRC6B	NM_015088.3	c.3791-464C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNRC6B	ENST00000454349.7	c.4121-464C>T		intron_variant		2	NM_001162501.2	P3

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101304 AN: 151946 Hom.: 35701 Cov.: 31

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.667 AC: 101437 AN: 152064 Hom.: 35776 Cov.: 31 AF XY: 0.666 AC XY: 49508 AN XY: 74308

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.588

Alfa AF: 0.603 Hom.: 6570

Bravo AF: 0.676

Asia WGS AF: 0.663 AC: 2307 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	2.0
Dann	Benign	0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs139911; hg19: chr22-40704052;