19-1611732-G-C

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1

The NM_003200.5(TCF3):ā€‹c.1940C>Gā€‹(p.Ala647Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000477 in 1,613,546 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: š‘“ 0.00020 ( 0 hom., cov: 30)
Exomes š‘“: 0.000031 ( 0 hom. )

Consequence

TCF3
NM_003200.5 missense

Scores

19

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:1

Conservation

PhyloP100: 5.11
Variant links:
Genes affected
TCF3 (HGNC:11633): (transcription factor 3) This gene encodes a member of the E protein (class I) family of helix-loop-helix transcription factors. E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and are inhibited by heterodimerization with inhibitor of DNA-binding (class IV) helix-loop-helix proteins. E proteins play a critical role in lymphopoiesis, and the encoded protein is required for B and T lymphocyte development. Deletion of this gene or diminished activity of the encoded protein may play a role in lymphoid malignancies. This gene is also involved in several chromosomal translocations that are associated with lymphoid malignancies including pre-B-cell acute lymphoblastic leukemia (t(1;19), with PBX1), childhood leukemia (t(19;19), with TFPT) and acute leukemia (t(12;19), with ZNF384). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Sep 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.03769034).
BP6
Variant 19-1611732-G-C is Benign according to our data. Variant chr19-1611732-G-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1598229.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000204 (31/152110) while in subpopulation AFR AF= 0.000701 (29/41388). AF 95% confidence interval is 0.0005. There are 0 homozygotes in gnomad4. There are 15 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TCF3NM_003200.5 linkc.1940C>G p.Ala647Gly missense_variant Exon 19 of 19 ENST00000262965.12 NP_003191.1 P15923-1
TCF3NM_001136139.4 linkc.1931C>G p.Ala644Gly missense_variant Exon 19 of 20 ENST00000588136.7 NP_001129611.1 P15923-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TCF3ENST00000262965.12 linkc.1940C>G p.Ala647Gly missense_variant Exon 19 of 19 1 NM_003200.5 ENSP00000262965.5 P15923-1
TCF3ENST00000588136.7 linkc.1931C>G p.Ala644Gly missense_variant Exon 19 of 20 2 NM_001136139.4 ENSP00000468487.1 P15923-2

Frequencies

GnomAD3 genomes
AF:
0.000204
AC:
31
AN:
152110
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.000701
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000961
GnomAD3 exomes
AF:
0.0000639
AC:
16
AN:
250328
Hom.:
0
AF XY:
0.0000148
AC XY:
2
AN XY:
135566
show subpopulations
Gnomad AFR exome
AF:
0.000865
Gnomad AMR exome
AF:
0.0000579
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000315
AC:
46
AN:
1461436
Hom.:
0
Cov.:
31
AF XY:
0.0000275
AC XY:
20
AN XY:
727012
show subpopulations
Gnomad4 AFR exome
AF:
0.00122
Gnomad4 AMR exome
AF:
0.0000224
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:
0.00
Gnomad4 OTH exome
AF:
0.0000662
GnomAD4 genome
AF:
0.000204
AC:
31
AN:
152110
Hom.:
0
Cov.:
30
AF XY:
0.000202
AC XY:
15
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.000701
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000961
Alfa
AF:
0.0000712
Hom.:
0
Bravo
AF:
0.000302
ESP6500AA
AF:
0.000908
AC:
4
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000741
AC:
9

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Oct 19, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1940C>G (p.A647G) alteration is located in exon 19 (coding exon 18) of the TCF3 gene. This alteration results from a C to G substitution at nucleotide position 1940, causing the alanine (A) at amino acid position 647 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

not provided Benign:1
Feb 14, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.077
BayesDel_addAF
Benign
-0.38
T
BayesDel_noAF
Benign
-0.38
CADD
Benign
19
DANN
Benign
0.96
DEOGEN2
Benign
0.21
T;T;T;T;T;T;.;.;.
Eigen
Benign
-0.35
Eigen_PC
Benign
-0.17
FATHMM_MKL
Benign
0.72
D
LIST_S2
Benign
0.85
T;T;T;.;T;T;T;T;T
M_CAP
Benign
0.0092
T
MetaRNN
Benign
0.038
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
-0.76
N;.;.;N;.;.;.;.;.
PrimateAI
Benign
0.39
T
PROVEAN
Benign
0.49
N;.;.;.;.;.;.;.;N
REVEL
Benign
0.18
Sift
Benign
0.32
T;.;.;.;.;.;.;.;T
Sift4G
Benign
0.58
T;T;T;T;T;T;T;T;T
Polyphen
0.79
P;.;.;P;.;.;.;B;.
Vest4
0.053
MVP
0.47
MPC
0.14
ClinPred
0.034
T
GERP RS
3.5
Varity_R
0.048
gMVP
0.35

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

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: rs142145295; hg19: chr19-1611731; API