7-5316217-C-T

Position:

• chr7-5316217-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001080495.3(TNRC18):​c.6746-145G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 537,080 control chromosomes in the GnomAD database, including 194,474 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.85 (53606 hom., cov: 24)
  • Exomes 𝑓: 0.85 (140868 hom.)
• Consequence: TNRC18 NM_001080495.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.833

Genes affected

TNRC18 (HGNC:11962): (trinucleotide repeat containing 18) Predicted to enable chromatin binding activity. Located in cytosol; mitochondrion; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BP6: Variant 7-5316217-C-T is Benign according to our data. Variant chr7-5316217-C-T is described in ClinVar as [Benign]. Clinvar id is 1291078.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNRC18	NM_001080495.3	c.6746-145G>A		intron_variant		ENST00000430969.6	NP_001073964.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNRC18	ENST00000430969.6	c.6746-145G>A		intron_variant		5	NM_001080495.3	ENSP00000395538	P4
TNRC18	ENST00000328270.3	c.186-145G>A		intron_variant		5		ENSP00000329902
TNRC18	ENST00000399537.8	c.6746-145G>A		intron_variant		5		ENSP00000382452	A2

Frequencies

GnomAD3 genomes AF: 0.845 AC: 126548 AN: 149756 Hom.: 53563 Cov.: 24

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.824

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.851

GnomAD4 exome AF: 0.853 AC: 330205 AN: 387210 Hom.: 140868 AF XY: 0.850 AC XY: 174954 AN XY: 205738

Gnomad4 AFR exome AF: 0.821

Gnomad4 AMR exome AF: 0.869

Gnomad4 ASJ exome AF: 0.841

Gnomad4 EAS exome AF: 0.965

Gnomad4 SAS exome AF: 0.825

Gnomad4 FIN exome AF: 0.878

Gnomad4 NFE exome AF: 0.845

Gnomad4 OTH exome AF: 0.848

GnomAD4 genome AF: 0.845 AC: 126644 AN: 149870 Hom.: 53606 Cov.: 24 AF XY: 0.848 AC XY: 61864 AN XY: 72974

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.853

Alfa AF: 0.850 Hom.: 9507

Bravo AF: 0.845

Asia WGS AF: 0.891 AC: 3097 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.63

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: rs4236384; hg19: chr7-5355848;