Variant 2-85133705-GGGCGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_031283.3(TCF7L1):c.37_42dupGGCGGC(p.Gly13_Gly14dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0075 ( 12 hom., cov: 0)

Exomes 𝑓: 0.0092 ( 35 hom. )

Consequence

TCF7L1
NM_031283.3 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0880

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 Likely_benign. Variant got -4 ACMG points.

BS2

High AC in GnomAd4 at 1101 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCF7L1	NM_031283.3 link	c.37_42dupGGCGGC	p.Gly13_Gly14dup	conservative_inframe_insertion	Exon 1 of 12	ENST00000282111.4	NP_112573.1	Q9HCS4
TCF7L1	XM_006712109.3 link	c.37_42dupGGCGGC	p.Gly13_Gly14dup	conservative_inframe_insertion	Exon 1 of 12		XP_006712172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCF7L1	ENST00000282111.4 link	c.37_42dupGGCGGC	p.Gly13_Gly14dup	conservative_inframe_insertion	Exon 1 of 12	1	NM_031283.3	ENSP00000282111.3		Q9HCS4

Frequencies

GnomAD3 genomes

AF:

0.00755

AC:

1101

AN:

145806

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00155

Gnomad AMI

AF:

0.00885

Gnomad AMR

AF:

0.00156

Gnomad ASJ

AF:

0.00207

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000628

Gnomad FIN

AF:

0.0411

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00979

Gnomad OTH

AF:

0.00248

GnomAD3 exomes

AF:

0.00385

AC:

AN:

520

Hom.:

AF XY:

0.00333

AC XY:

AN XY:

300

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00422

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00925

AC:

8608

AN:

930778

Hom.:

Cov.:

AF XY:

0.00913

AC XY:

3991

AN XY:

437296

show subpopulations

Gnomad4 AFR exome

AF:

0.000871

Gnomad4 AMR exome

AF:

0.00156

Gnomad4 ASJ exome

AF:

0.00107

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000609

Gnomad4 FIN exome

AF:

0.0124

Gnomad4 NFE exome

AF:

0.00999

Gnomad4 OTH exome

AF:

0.00586

GnomAD4 genome

AF:

0.00755

AC:

1101

AN:

145914

Hom.:

Cov.:

AF XY:

0.00872

AC XY:

619

AN XY:

70968

show subpopulations

Gnomad4 AFR

AF:

0.00155

Gnomad4 AMR

AF:

0.00156

Gnomad4 ASJ

AF:

0.00207

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000629

Gnomad4 FIN

AF:

0.0411

Gnomad4 NFE

AF:

0.00979

Gnomad4 OTH

AF:

0.00245

Bravo

AF:

0.00472

ClinVar

Not reported in ClinVar

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over