22-40219272-G-T

Position:

• chr22-40219272-G-T

Variant summary

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

The NM_001162501.2(TNRC6B):​c.6-26743G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,072 control chromosomes in the GnomAD database, including 7,592 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 0.29 (7592 hom., cov: 31)
• Consequence: TNRC6B NM_001162501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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]

TNRC6B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNRC6B	NM_001162501.2	c.6-26743G>T		intron_variant		ENST00000454349.7	NP_001155973.1
TNRC6B	NM_015088.3	c.6-26743G>T		intron_variant			NP_055903.2
TNRC6B	NM_001024843.2	c.114-26743G>T		intron_variant			NP_001020014.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNRC6B	ENST00000454349.7	c.6-26743G>T		intron_variant		2	NM_001162501.2	ENSP00000401946.2

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44591 AN: 151954 Hom.: 7582 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.293 AC: 44620 AN: 152072 Hom.: 7592 Cov.: 31 AF XY: 0.302 AC XY: 22416 AN XY: 74340

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.291

Alfa AF: 0.334 Hom.: 4241

Bravo AF: 0.291

Asia WGS AF: 0.464 AC: 1612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.089
DANN	Benign	0.59

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: rs739182; hg19: chr22-40615276;