Variant 2-85283271-C-CCCG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_031283.3(TCF7L1):c.442-222_442-221insGCC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.30 ( 7655 hom., cov: 0)

Consequence

TCF7L1
NM_031283.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.369

Variant links:

Genes affected

TCF7L1 (HGNC:11640): (transcription factor 7 like 1) This gene encodes a member of the T cell factor/lymphoid enhancer factor family of transcription factors. These transcription factors are activated by beta catenin, mediate the Wnt signaling pathway and are antagonized by the transforming growth factor beta signaling pathway. The encoded protein contains a high mobility group-box DNA binding domain and participates in the regulation of cell cycle genes and cellular senescence. [provided by RefSeq, Nov 2010]

TCF7L1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 2-85283271-C-CCCG is Benign according to our data. Variant chr2-85283271-C-CCCG is described in ClinVar as [Benign]. Clinvar id is 1222639.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TCF7L1	NM_031283.3 linkuse as main transcript	c.442-222_442-221insGCC		intron_variant		ENST00000282111.4	NP_112573.1
TCF7L1	XM_006712109.3 linkuse as main transcript	c.442-222_442-221insGCC		intron_variant			XP_006712172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TCF7L1	ENST00000282111.4 linkuse as main transcript	c.442-222_442-221insGCC		intron_variant		1	NM_031283.3	ENSP00000282111	P1
TCF7L1	ENST00000442813.1 linkuse as main transcript	c.-9-222_-9-221insGCC		intron_variant		5		ENSP00000388984

Frequencies

GnomAD3 genomes

AF:

0.296

AC:

44323

AN:

149906

Hom.:

7653

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.273

Gnomad ASJ

AF:

0.440

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.301

Gnomad FIN

AF:

0.331

Gnomad MID

AF:

0.362

Gnomad NFE

AF:

0.395

Gnomad OTH

AF:

0.309

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

GnomAD4 genome

AF:

0.296

AC:

44344

AN:

150018

Hom.:

7655

Cov.:

AF XY:

0.291

AC XY:

21318

AN XY:

73192

show subpopulations

Gnomad4 AFR

AF:

0.114

Gnomad4 AMR

AF:

0.273

Gnomad4 ASJ

AF:

0.440

Gnomad4 EAS

AF:

0.275

Gnomad4 SAS

AF:

0.300

Gnomad4 FIN

AF:

0.331

Gnomad4 NFE

AF:

0.395

Gnomad4 OTH

AF:

0.309

Alfa

AF:

0.164

Hom.:

264

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over