2-85133705-GGGCGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGC

Variant summary

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

The NM_031283.3(TCF7L1):​c.40_42dupGGC​(p.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 0.00014 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00013 ( 0 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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAd4 at 21 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TCF7L1NM_031283.3 linkc.40_42dupGGC p.Gly14dup conservative_inframe_insertion Exon 1 of 12 ENST00000282111.4 NP_112573.1 Q9HCS4
TCF7L1XM_006712109.3 linkc.40_42dupGGC p.Gly14dup conservative_inframe_insertion Exon 1 of 12 XP_006712172.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TCF7L1ENST00000282111.4 linkc.40_42dupGGC p.Gly14dup conservative_inframe_insertion Exon 1 of 12 1 NM_031283.3 ENSP00000282111.3 Q9HCS4

Frequencies

GnomAD3 genomes
AF:
0.000144
AC:
21
AN:
145814
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000740
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000340
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000400
Gnomad SAS
AF:
0.000209
Gnomad FIN
AF:
0.000118
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000137
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000126
AC:
117
AN:
930918
Hom.:
0
Cov.:
0
AF XY:
0.000123
AC XY:
54
AN XY:
437368
show subpopulations
Gnomad4 AFR exome
AF:
0.0000544
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000277
Gnomad4 FIN exome
AF:
0.0000855
Gnomad4 NFE exome
AF:
0.000129
Gnomad4 OTH exome
AF:
0.0000598
GnomAD4 genome
AF:
0.000144
AC:
21
AN:
145814
Hom.:
0
Cov.:
0
AF XY:
0.000155
AC XY:
11
AN XY:
70850
show subpopulations
Gnomad4 AFR
AF:
0.0000740
Gnomad4 AMR
AF:
0.000340
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000400
Gnomad4 SAS
AF:
0.000209
Gnomad4 FIN
AF:
0.000118
Gnomad4 NFE
AF:
0.000137
Gnomad4 OTH
AF:
0.00

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.

Other links and lift over

dbSNP: rs566806913; hg19: chr2-85360828; API