7-19117045-TGCCGCCGCCGCCGCCCGCGCCGCC-TGCCGCCGCCGCCGCCCGCGCCGCCGCCGCCGCCGCCGCCCGCGCCGCC

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM1BS2

The NM_000474.4(TWIST1):​c.253_276dupGGCGGCGCGGGCGGCGGCGGCGGC​(p.Gly92_Ser93insGlyGlyAlaGlyGlyGlyGlyGly) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000345 in 150,842 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00034 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000016 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TWIST1
NM_000474.4 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.251
Variant links:
Genes affected
TWIST1 (HGNC:12428): (twist family bHLH transcription factor 1) This gene encodes a basic helix-loop-helix (bHLH) transcription factor that plays an important role in embryonic development. The encoded protein forms both homodimers and heterodimers that bind to DNA E box sequences and regulate the transcription of genes involved in cranial suture closure during skull development. This protein may also regulate neural tube closure, limb development and brown fat metabolism. This gene is hypermethylated and overexpressed in multiple human cancers, and the encoded protein promotes tumor cell invasion and metastasis, as well as metastatic recurrence. Mutations in this gene cause Saethre-Chotzen syndrome in human patients, which is characterized by craniosynostosis, ptosis and hypertelorism. [provided by RefSeq, Jul 2020]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM1
In a chain Twist-related protein 1 (size 201) in uniprot entity TWST1_HUMAN there are 17 pathogenic changes around while only 3 benign (85%) in NM_000474.4
BS2
High AC in GnomAd4 at 52 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TWIST1NM_000474.4 linkc.253_276dupGGCGGCGCGGGCGGCGGCGGCGGC p.Gly92_Ser93insGlyGlyAlaGlyGlyGlyGlyGly conservative_inframe_insertion 1/2 ENST00000242261.6 NP_000465.1 Q15672
TWIST1NR_149001.2 linkn.568_591dupGGCGGCGCGGGCGGCGGCGGCGGC non_coding_transcript_exon_variant 1/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TWIST1ENST00000242261.6 linkc.253_276dupGGCGGCGCGGGCGGCGGCGGCGGC p.Gly92_Ser93insGlyGlyAlaGlyGlyGlyGlyGly conservative_inframe_insertion 1/21 NM_000474.4 ENSP00000242261.5 Q15672
TWIST1ENST00000354571.5 linkn.49_72dupGGCGGCGCGGGCGGCGGCGGCGGC non_coding_transcript_exon_variant 1/32 ENSP00000346582.5 H7BY00

Frequencies

GnomAD3 genomes
AF:
0.000345
AC:
52
AN:
150740
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00109
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000330
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000195
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000484
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000162
AC:
21
AN:
1292790
Hom.:
0
Cov.:
31
AF XY:
0.0000110
AC XY:
7
AN XY:
636940
show subpopulations
Gnomad4 AFR exome
AF:
0.000505
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000331
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000288
Gnomad4 OTH exome
AF:
0.0000748
GnomAD4 genome
AF:
0.000345
AC:
52
AN:
150842
Hom.:
0
Cov.:
32
AF XY:
0.000285
AC XY:
21
AN XY:
73642
show subpopulations
Gnomad4 AFR
AF:
0.00109
Gnomad4 AMR
AF:
0.000330
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000196
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000478

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Saethre-Chotzen syndrome;C4551902:TWIST1-related craniosynostosis Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 28, 2021This variant, c.253_276dup, results in the insertion of 8 amino acid(s) to the TWIST1 protein (p.Gly85_Gly92dup), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This variant has not been reported in the literature in individuals affected with TWIST1-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

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: rs544465774; hg19: chr7-19156668; API