rs2311001

Variant names:

• chr17-78096472-G-C
• rs2311001
• NM_001142640.2:c.4928-1273G>C

Your query was ambiguous. Multiple possible variants found:

• chr17-78096472-G-C
• chr17-78096472-G-T

Variant summary

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

The NM_001142640.2(TNRC6C):​c.4928-1273G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 152,084 control chromosomes in the GnomAD database, including 17,809 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 0.46 (17809 hom., cov: 33)
• Consequence: TNRC6C NM_001142640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNRC6C	NM_001142640.2	MANE Select	c.4928-1273G>C		intron	N/A	NP_001136112.2	Q9HCJ0-3
	TNRC6C	NM_001395509.1		c.4952-1871G>C		intron	N/A	NP_001382438.1
	TNRC6C	NM_001395510.1		c.4928-1871G>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.4928-1273G>C		intron	N/A	ENSP00000512514.1	Q9HCJ0-3
	TNRC6C	ENST00000935186.1		c.4928-1213G>C		intron	N/A	ENSP00000605245.1
	TNRC6C	ENST00000636222.1	TSL:5	c.4952-1273G>C		intron	N/A	ENSP00000489933.1	A0A1B0GU24

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70409 AN: 151966 Hom.: 17763 Cov.: 33

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.464 AC: 70522 AN: 152084 Hom.: 17809 Cov.: 33 AF XY: 0.467 AC XY: 34689 AN XY: 74324

African (AFR) AF: 0.669 AC: 27766 AN: 41480

American (AMR) AF: 0.461 AC: 7041 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1360 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2607 AN: 5178

South Asian (SAS) AF: 0.491 AC: 2371 AN: 4830

European-Finnish (FIN) AF: 0.384 AC: 4056 AN: 10566

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23697 AN: 67962

Other (OTH) AF: 0.473 AC: 998 AN: 2110

Alfa AF: 0.414 Hom.: 1753

Bravo AF: 0.483

Asia WGS AF: 0.512 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29
DANN	Benign	0.42
PhyloP100		-0.32
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: rs2311001; hg19: chr17-76092553;