rs4236384

Variant names:

• chr7-5316217-C-T
• rs4236384
• NM_001080495.3:c.6746-145G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-5316217-C-T
• chr7-5316217-C-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080495.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNRC18	NM_001080495.3	MANE Select	c.6746-145G>A		intron	N/A	NP_001073964.2	O15417-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNRC18	ENST00000430969.6	TSL:5 MANE Select	c.6746-145G>A		intron	N/A	ENSP00000395538.1	O15417-1
	TNRC18	ENST00000399537.8	TSL:5	c.6746-145G>A		intron	N/A	ENSP00000382452.4	H9KVB4
	TNRC18	ENST00000328270.3	TSL:5	c.185-145G>A		intron	N/A	ENSP00000329902.3	H7BXS9

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

African (AFR) AF: 0.821 AC: 6608 AN: 8044

American (AMR) AF: 0.869 AC: 7735 AN: 8906

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 10761 AN: 12800

East Asian (EAS) AF: 0.965 AC: 22217 AN: 23016

South Asian (SAS) AF: 0.825 AC: 28104 AN: 34056

European-Finnish (FIN) AF: 0.878 AC: 26424 AN: 30096

Middle Eastern (MID) AF: 0.846 AC: 1556 AN: 1840

European-Non Finnish (NFE) AF: 0.845 AC: 207429 AN: 245618

Other (OTH) AF: 0.848 AC: 19371 AN: 22834

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

African (AFR) AF: 0.816 AC: 33098 AN: 40538

American (AMR) AF: 0.862 AC: 12890 AN: 14952

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2857 AN: 3468

East Asian (EAS) AF: 0.968 AC: 4859 AN: 5022

South Asian (SAS) AF: 0.829 AC: 3946 AN: 4760

European-Finnish (FIN) AF: 0.891 AC: 8952 AN: 10050

Middle Eastern (MID) AF: 0.821 AC: 238 AN: 290

European-Non Finnish (NFE) AF: 0.845 AC: 57270 AN: 67800

Other (OTH) AF: 0.853 AC: 1777 AN: 2084

Alfa AF: 0.853 Hom.: 11201

Bravo AF: 0.845

Asia WGS AF: 0.891 AC: 3097 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.63
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4236384;

hg19: chr7-5355848;