chr17-78053294-G-A

Variant names:

• chr17-78053294-G-A
• rs12601622
• NM_001142640.2:c.3016+1846G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142640.2(TNRC6C):​c.3016+1846G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.019 in 152,216 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.019 (46 hom., cov: 32)
• Consequence: TNRC6C NM_001142640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 1 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0725 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNRC6C	NM_001142640.2	MANE Select	c.3016+1846G>A		intron	N/A	NP_001136112.2
	TNRC6C	NM_001395509.1		c.3016+1846G>A		intron	N/A	NP_001382438.1
	TNRC6C	NM_001395510.1		c.3016+1846G>A		intron	N/A	NP_001382439.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNRC6C	ENST00000696270.1	MANE Select	c.3016+1846G>A		intron	N/A	ENSP00000512514.1
	TNRC6C	ENST00000636222.1	TSL:5	c.3016+1846G>A		intron	N/A	ENSP00000489933.1
	TNRC6C	ENST00000696541.1		c.3016+1846G>A		intron	N/A	ENSP00000512702.1

Frequencies

GnomAD3 genomes AF: 0.0190 AC: 2888 AN: 152098 Hom.: 46 Cov.: 32

Gnomad AFR AF: 0.00391

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0193

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.0153

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0222

Gnomad OTH AF: 0.0268

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0190 AC: 2889 AN: 152216 Hom.: 46 Cov.: 32 AF XY: 0.0189 AC XY: 1405 AN XY: 74438

African (AFR) AF: 0.00390 AC: 162 AN: 41540

American (AMR) AF: 0.0193 AC: 295 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3472

East Asian (EAS) AF: 0.0788 AC: 408 AN: 5176

South Asian (SAS) AF: 0.0286 AC: 138 AN: 4820

European-Finnish (FIN) AF: 0.0153 AC: 162 AN: 10592

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0222 AC: 1511 AN: 68002

Other (OTH) AF: 0.0270 AC: 57 AN: 2110

Alfa AF: 0.0213 Hom.: 92

Bravo AF: 0.0190

Asia WGS AF: 0.0520 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.57
PhyloP100		-0.062
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

Other links and lift over

dbSNP: rs12601622; hg19: chr17-76049375;