7-5308851-A-C

Variant names:

• chr7-5308851-A-C
• rs746360360
• NM_001080495.3:c.8700+24T>G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001080495.3(TNRC18):​c.8700+24T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0063 (0 hom., cov: 0)
  • Exomes 𝑓: 0.16 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TNRC18 NM_001080495.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.768

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 Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 7-5308851-A-C is Benign according to our data. Variant chr7-5308851-A-C is described in ClinVar as [Benign]. Clinvar id is 1242552.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNRC18	NM_001080495.3	c.8700+24T>G		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.8700+24T>G		intron_variant	Intron 29 of 29	5	NM_001080495.3	ENSP00000395538.1
TNRC18	ENST00000399537.8	c.8700+24T>G		intron_variant	Intron 29 of 29	5		ENSP00000382452.4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 219 AN: 34774 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00745

Gnomad AMI AF: 0.00746

Gnomad AMR AF: 0.00681

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.00422

Gnomad FIN AF: 0.0105

Gnomad MID AF: 0.0114

Gnomad NFE AF: 0.00575

Gnomad OTH AF: 0.0158

GnomAD3 exomes AF: 0.0139 AC: 960 AN: 68862 Hom.: 0 AF XY: 0.0128 AC XY: 492 AN XY: 38316

Gnomad AFR exome AF: 0.00391

Gnomad AMR exome AF: 0.0569

Gnomad ASJ exome AF: 0.0120

Gnomad EAS exome AF: 0.0380

Gnomad SAS exome AF: 0.0136

Gnomad FIN exome AF: 0.00301

Gnomad NFE exome AF: 0.00753

Gnomad OTH exome AF: 0.0251

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.164 AC: 37399 AN: 228612 Hom.: 0 Cov.: 8 AF XY: 0.151 AC XY: 17575 AN XY: 116120

Gnomad4 AFR exome AF: 0.152

Gnomad4 AMR exome AF: 0.163

Gnomad4 ASJ exome AF: 0.0798

Gnomad4 EAS exome AF: 0.0635

Gnomad4 SAS exome AF: 0.0906

Gnomad4 FIN exome AF: 0.0187

Gnomad4 NFE exome AF: 0.194

Gnomad4 OTH exome AF: 0.150

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00632 AC: 220 AN: 34820 Hom.: 0 Cov.: 0 AF XY: 0.00567 AC XY: 99 AN XY: 17464

Gnomad4 AFR AF: 0.00754

Gnomad4 AMR AF: 0.00680

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.00419

Gnomad4 FIN AF: 0.0105

Gnomad4 NFE AF: 0.00575

Gnomad4 OTH AF: 0.0155

Alfa AF: 0.00261 Hom.: 0

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 04, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.40

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: rs746360360; hg19: chr7-5348482;