7-5308345-T-TG

Variant names:

• chr7-5308345-T-TG
• rs148493175
• NM_001080495.3:c.8701-34dupC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001080495.3(TNRC18):​c.8701-34dupC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,579,180 control chromosomes in the GnomAD database, including 18,749 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.13 (1900 hom., cov: 31)
  • Exomes 𝑓: 0.13 (16849 hom.)
• Consequence: TNRC18 NM_001080495.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.125

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 -10 ACMG points.

• BP6: Variant 7-5308345-T-TG is Benign according to our data. Variant chr7-5308345-T-TG is described in ClinVar as [Benign]. Clinvar id is 1281096.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNRC18	NM_001080495.3	c.8701-34dupC		intron_variant	Intron 29 of 29	ENST00000430969.6	NP_001073964.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNRC18	ENST00000430969.6	c.8701-34_8701-33insC		intron_variant	Intron 29 of 29	5	NM_001080495.3	ENSP00000395538.1
TNRC18	ENST00000399537.8	c.8701-34_8701-33insC		intron_variant	Intron 29 of 29	5		ENSP00000382452.4

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19785 AN: 150588 Hom.: 1902 Cov.: 31

Gnomad AFR AF: 0.0981

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0959

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.112

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.142

GnomAD3 exomes AF: 0.102 AC: 17384 AN: 171094 Hom.: 2485 AF XY: 0.0981 AC XY: 9015 AN XY: 91916

Gnomad AFR exome AF: 0.0594

Gnomad AMR exome AF: 0.107

Gnomad ASJ exome AF: 0.0430

Gnomad EAS exome AF: 0.479

Gnomad SAS exome AF: 0.168

Gnomad FIN exome AF: 0.0803

Gnomad NFE exome AF: 0.0468

Gnomad OTH exome AF: 0.0902

GnomAD4 exome AF: 0.128 AC: 182790 AN: 1428470 Hom.: 16849 Cov.: 32 AF XY: 0.131 AC XY: 93032 AN XY: 707936

Gnomad4 AFR exome AF: 0.0912

Gnomad4 AMR exome AF: 0.163

Gnomad4 ASJ exome AF: 0.0970

Gnomad4 EAS exome AF: 0.527

Gnomad4 SAS exome AF: 0.280

Gnomad4 FIN exome AF: 0.137

Gnomad4 NFE exome AF: 0.102

Gnomad4 OTH exome AF: 0.146

GnomAD4 genome AF: 0.131 AC: 19796 AN: 150710 Hom.: 1900 Cov.: 31 AF XY: 0.140 AC XY: 10329 AN XY: 73656

Gnomad4 AFR AF: 0.0982

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.0959

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.145

Bravo AF: 0.126

Asia WGS AF: 0.403 AC: 1400 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 17, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs148493175; hg19: chr7-5347976;