chr20-2320662-T-G

Variant summary

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

The NM_003245.4(TGM3):​c.983+3177T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,074 control chromosomes in the GnomAD database, including 49,966 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 0.81 ( 49966 hom., cov: 31)

Consequence

TGM3
NM_003245.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.155
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=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TGM3NM_003245.4 linkuse as main transcriptc.983+3177T>G intron_variant ENST00000381458.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TGM3ENST00000381458.6 linkuse as main transcriptc.983+3177T>G intron_variant 1 NM_003245.4 P1
TGM3ENST00000463090.1 linkuse as main transcriptn.363+3177T>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.810
AC:
123029
AN:
151956
Hom.:
49911
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.789
Gnomad AMI
AF:
0.784
Gnomad AMR
AF:
0.863
Gnomad ASJ
AF:
0.790
Gnomad EAS
AF:
0.956
Gnomad SAS
AF:
0.837
Gnomad FIN
AF:
0.813
Gnomad MID
AF:
0.722
Gnomad NFE
AF:
0.798
Gnomad OTH
AF:
0.810
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.810
AC:
123142
AN:
152074
Hom.:
49966
Cov.:
31
AF XY:
0.810
AC XY:
60230
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.789
Gnomad4 AMR
AF:
0.863
Gnomad4 ASJ
AF:
0.790
Gnomad4 EAS
AF:
0.956
Gnomad4 SAS
AF:
0.836
Gnomad4 FIN
AF:
0.813
Gnomad4 NFE
AF:
0.798
Gnomad4 OTH
AF:
0.812
Alfa
AF:
0.798
Hom.:
62264
Bravo
AF:
0.813
Asia WGS
AF:
0.911
AC:
3168
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
4.2
DANN
Benign
0.43

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: rs84823; hg19: chr20-2301308; API