rs504417

chr15-43262028-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_201631.4(TGM5):c.11-1449T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,978 control chromosomes in the GnomAD database, including 22,047 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 0.48 (22047 hom., cov: 32)
• Consequence: TGM5 NM_201631.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

Genes affected

TGM5 (HGNC:11781): (transglutaminase 5) This gene encodes a member of the transglutaminase family. The encoded protein catalyzes formation of protein cross-links between glutamine and lysine residues, often resulting in stabilization of protein assemblies. This reaction is calcium dependent. Mutations in this gene have been associated with acral peeling skin syndrome. [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TGM5	NM_201631.4	c.11-1449T>C		intron_variant		ENST00000220420.10
TGM5	NM_004245.4	c.11-1449T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TGM5	ENST00000220420.10	c.11-1449T>C		intron_variant		1	NM_201631.4	P1
TGM5	ENST00000349114.8	c.11-1449T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72321 AN: 151860 Hom.: 21988 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.442

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.477 AC: 72436 AN: 151978 Hom.: 22047 Cov.: 32 AF XY: 0.468 AC XY: 34740 AN XY: 74284

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.446

Alfa AF: 0.368 Hom.: 5416

Bravo AF: 0.508

Asia WGS AF: 0.441 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.12
Dann	Benign	0.55

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

Other links and lift over

dbSNP: rs504417; hg19: chr15-43554226;