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GeneBe

rs7901695

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001367943(TCF7L2):c.450+29705T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151992 control chromosomes in the gnomAD Genomes database, including 9107 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 0.33 ( 9107 hom., cov: 32)

Consequence

TCF7L2
NM_001367943 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.776

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TCF7L2NM_001367943.1 linkuse as main transcriptc.450+29705T>C intron_variant ENST00000355995.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TCF7L2ENST00000355995.9 linkuse as main transcriptc.450+29705T>C intron_variant 1 NM_001367943.1 Q9NQB0-1

Frequencies

GnomAD3 genomes
AF:
0.333
AC:
50674
AN:
151992
Hom.:
9107
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.455
Gnomad AMI
AF:
0.272
Gnomad AMR
AF:
0.297
Gnomad ASJ
AF:
0.307
Gnomad EAS
AF:
0.0264
Gnomad SAS
AF:
0.301
Gnomad FIN
AF:
0.217
Gnomad MID
AF:
0.405
Gnomad NFE
AF:
0.312
Gnomad OTH
AF:
0.370
Alfa
AF:
0.310
Hom.:
16637
Bravo
AF:
0.340
Asia WGS
AF:
0.167
AC:
588
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
0.72
Dann
Benign
0.65

Splicing

Find out SpliceAI 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: rs7901695; hg19: chr10-114754088;