rs527665020

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_207037.2(TCF12):​c.75+58_75+65delGTTTGTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000248 in 1,605,812 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00015 ( 0 hom. )

Consequence

TCF12
NM_207037.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.54
Variant links:
Genes affected
TCF12 (HGNC:11623): (transcription factor 12) The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00118 (180/151940) while in subpopulation AFR AF= 0.00417 (173/41446). AF 95% confidence interval is 0.00367. There are 0 homozygotes in gnomad4. There are 87 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High AC in GnomAd4 at 180 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TCF12NM_207037.2 linkc.75+58_75+65delGTTTGTTT intron_variant Intron 2 of 20 ENST00000333725.10 NP_996920.1 Q99081-3A0A024R5Z0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TCF12ENST00000333725.10 linkc.75+43_75+50delTTTGTTTG intron_variant Intron 2 of 20 1 NM_207037.2 ENSP00000331057.6 Q99081-3

Frequencies

GnomAD3 genomes
AF:
0.00118
AC:
179
AN:
151822
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.00416
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
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:
0.0000294
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.000324
AC:
80
AN:
246558
Hom.:
0
AF XY:
0.000233
AC XY:
31
AN XY:
133210
show subpopulations
Gnomad AFR exome
AF:
0.00421
Gnomad AMR exome
AF:
0.000118
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000331
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000630
Gnomad OTH exome
AF:
0.000167
GnomAD4 exome
AF:
0.000151
AC:
219
AN:
1453872
Hom.:
0
AF XY:
0.000142
AC XY:
103
AN XY:
723710
show subpopulations
Gnomad4 AFR exome
AF:
0.00417
Gnomad4 AMR exome
AF:
0.000157
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000814
Gnomad4 FIN exome
AF:
0.0000188
Gnomad4 NFE exome
AF:
0.0000344
Gnomad4 OTH exome
AF:
0.000399
GnomAD4 genome
AF:
0.00118
AC:
180
AN:
151940
Hom.:
0
Cov.:
30
AF XY:
0.00117
AC XY:
87
AN XY:
74252
show subpopulations
Gnomad4 AFR
AF:
0.00417
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00142
Bravo
AF:
0.00127

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: rs527665020; hg19: chr15-57212228; API