chr7-45107057-C-A

Position:

• chr7-45107057-C-A

Variant summary

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

The ENST00000258770.8(TBRG4):​c.412-1293G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 151,828 control chromosomes in the GnomAD database, including 37,379 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 0.70 (37369 hom., cov: 30)
  • Exomes 𝑓: 0.83 (10 hom.)
• Consequence: TBRG4 ENST00000258770.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

TBRG4 (HGNC:17443): (transforming growth factor beta regulator 4) Enables RNA binding activity. Involved in mitochondrial mRNA processing and regulation of mitochondrial mRNA stability. Located in mitochondrial matrix. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBRG4	NM_004749.4	c.412-1293G>T		intron_variant		ENST00000258770.8	NP_004740.2
TBRG4	NM_001261834.2	c.445-1293G>T		intron_variant			NP_001248763.1
TBRG4	NM_030900.4	c.412-1293G>T		intron_variant			NP_112162.1
TBRG4	NM_199122.3	c.412-1293G>T		intron_variant			NP_954573.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBRG4	ENST00000258770.8	c.412-1293G>T		intron_variant		1	NM_004749.4	ENSP00000258770	P1

Frequencies

GnomAD3 genomes AF: 0.699 AC: 105989 AN: 151682 Hom.: 37340 Cov.: 30

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.696

GnomAD4 exome AF: 0.833 AC: 25 AN: 30 Hom.: 10 Cov.: 0 AF XY: 0.818 AC XY: 18 AN XY: 22

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.699 AC: 106050 AN: 151798 Hom.: 37369 Cov.: 30 AF XY: 0.695 AC XY: 51593 AN XY: 74190

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.690

Alfa AF: 0.716 Hom.: 51686

Bravo AF: 0.692

Asia WGS AF: 0.579 AC: 2019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.54

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: rs3757572; hg19: chr7-45146656;