TNRC6C p.Ser1656Ser

Variant names:

• chr17-78097782-T-T
• ENST00000696270.1:c.

Your query was ambiguous. Multiple possible variants found:

• chr17-78097783--
• chr17-78097785-T-C
• chr17-78097785-T-A
• chr17-78097785-T-G
• chr17-78097783-TC-AG
• chr17-78097783-TCT-AGC

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001142640.2(TNRC6C):​c. variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TNRC6C NM_001142640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30
• Publications: 0 publications found

Genes affected

TNRC6C (HGNC:29318): (trinucleotide repeat containing adaptor 6C) Predicted to enable RNA binding activity. Involved in gene silencing by miRNA; positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay; and positive regulation of nuclear-transcribed mRNA poly(A) tail shortening. Predicted to be located in cytosol. Predicted to be active in P-body and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142640.2. 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
	TNRC6C	NM_001142640.2	MANE Select	c.		intron	N/A	NP_001136112.2	Q9HCJ0-3
	TNRC6C	NM_001395509.1		c.		intron	N/A	NP_001382438.1
	TNRC6C	NM_001395510.1		c.		intron	N/A	NP_001382439.1	Q9HCJ0-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNRC6C	ENST00000696270.1	MANE Select	c.		exon_region	Exon 19 of 23	ENSP00000512514.1	Q9HCJ0-3
	TNRC6C	ENST00000935186.1		c.		exon_region	Exon 19 of 23	ENSP00000605245.1
	TNRC6C	ENST00000636222.1	TSL:5	c.		exon_region	Exon 19 of 23	ENSP00000489933.1	A0A1B0GU24

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.3

Splicing

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

hg19: chr17-76093863;