2-85133705-GGGCGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC

Variant names:

• chr2-85133705-G-GGGCGGCGGCGGCGGC
• rs566806913
• NM_031283.3:c.28_42dupGGCGGCGGCGGCGGC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_031283.3(TCF7L1):​c.28_42dupGGCGGCGGCGGCGGC​(p.Gly10_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: not found (cov: 0)
  • Exomes 𝑓: 0.0000054 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TCF7L1 NM_031283.3 conservative_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCF7L1	NM_031283.3	c.28_42dupGGCGGCGGCGGCGGC	p.Gly10_Gly14dup	conservative_inframe_insertion	Exon 1 of 12	ENST00000282111.4	NP_112573.1
TCF7L1	XM_006712109.3	c.28_42dupGGCGGCGGCGGCGGC	p.Gly10_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	c.28_42dupGGCGGCGGCGGCGGC	p.Gly10_Gly14dup	conservative_inframe_insertion	Exon 1 of 12	1	NM_031283.3	ENSP00000282111.3

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000537 AC: 5 AN: 930944 Hom.: 0 Cov.: 0 AF XY: 0.00000229 AC XY: 1 AN XY: 437378

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000259

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000364

Gnomad4 OTH exome AF: 0.0000299

GnomAD4 genome Cov.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs566806913; hg19: chr2-85360828;