chr20-2338077-C-G

Variant summary

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

The NM_003245.4(TGM3):​c.1801-1777C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,042 control chromosomes in the GnomAD database, including 38,234 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 0.70 ( 38234 hom., cov: 32)

Consequence

TGM3
NM_003245.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.384
Variant links:
Genes affected
TGM3 (HGNC:11779): (transglutaminase 3) Transglutaminases are enzymes that catalyze the crosslinking of proteins by epsilon-gamma glutamyl lysine isopeptide bonds. While the primary structure of transglutaminases is not conserved, they all have the same amino acid sequence at their active sites and their activity is calcium-dependent. The protein encoded by this gene consists of two polypeptide chains activated from a single precursor protein by proteolysis. The encoded protein is involved the later stages of cell envelope formation in the epidermis and hair follicle. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TGM3NM_003245.4 linkuse as main transcriptc.1801-1777C>G intron_variant ENST00000381458.6 NP_003236.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TGM3ENST00000381458.6 linkuse as main transcriptc.1801-1777C>G intron_variant 1 NM_003245.4 ENSP00000370867 P1

Frequencies

GnomAD3 genomes
AF:
0.700
AC:
106355
AN:
151926
Hom.:
38184
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.856
Gnomad AMI
AF:
0.439
Gnomad AMR
AF:
0.701
Gnomad ASJ
AF:
0.510
Gnomad EAS
AF:
0.857
Gnomad SAS
AF:
0.743
Gnomad FIN
AF:
0.674
Gnomad MID
AF:
0.573
Gnomad NFE
AF:
0.609
Gnomad OTH
AF:
0.676
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.700
AC:
106460
AN:
152042
Hom.:
38234
Cov.:
32
AF XY:
0.705
AC XY:
52431
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.856
Gnomad4 AMR
AF:
0.702
Gnomad4 ASJ
AF:
0.510
Gnomad4 EAS
AF:
0.857
Gnomad4 SAS
AF:
0.743
Gnomad4 FIN
AF:
0.674
Gnomad4 NFE
AF:
0.609
Gnomad4 OTH
AF:
0.675
Alfa
AF:
0.557
Hom.:
1563
Bravo
AF:
0.708
Asia WGS
AF:
0.782
AC:
2714
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.29
DANN
Benign
0.39

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs214827; hg19: chr20-2318723; API