chr3-189863204-A-G

Position:

• chr3-189863204-A-G

Variant summary

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

The NM_003722.5(TP63):​c.580-1028A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,458 control chromosomes in the GnomAD database, including 27,731 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 0.60 (27731 hom., cov: 31)
• Consequence: TP63 NM_003722.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

TP63 (HGNC:15979): (tumor protein p63) This gene encodes a member of the p53 family of transcription factors. The functional domains of p53 family proteins include an N-terminal transactivation domain, a central DNA-binding domain and an oligomerization domain. Alternative splicing of this gene and the use of alternative promoters results in multiple transcript variants encoding different isoforms that vary in their functional properties. These isoforms function during skin development and maintenance, adult stem/progenitor cell regulation, heart development and premature aging. Some isoforms have been found to protect the germline by eliminating oocytes or testicular germ cells that have suffered DNA damage. Mutations in this gene are associated with ectodermal dysplasia, and cleft lip/palate syndrome 3 (EEC3); split-hand/foot malformation 4 (SHFM4); ankyloblepharon-ectodermal defects-cleft lip/palate; ADULT syndrome (acro-dermato-ungual-lacrimal-tooth); limb-mammary syndrome; Rap-Hodgkin syndrome (RHS); and orofacial cleft 8. [provided by RefSeq, Aug 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TP63	NM_001114980.2	c.298-1028A>G		intron_variant		ENST00000354600.10	NP_001108452.1
TP63	NM_003722.5	c.580-1028A>G		intron_variant		ENST00000264731.8	NP_003713.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TP63	ENST00000264731.8	c.580-1028A>G		intron_variant		1	NM_003722.5	ENSP00000264731	P4
TP63	ENST00000354600.10	c.298-1028A>G		intron_variant		1	NM_001114980.2	ENSP00000346614	A1

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90698 AN: 151342 Hom.: 27719 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.599 AC: 90745 AN: 151458 Hom.: 27731 Cov.: 31 AF XY: 0.591 AC XY: 43761 AN XY: 74020

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.589

Alfa AF: 0.581 Hom.: 3256

Bravo AF: 0.601

Asia WGS AF: 0.498 AC: 1735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	13
DANN	Benign	0.70

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: rs1913721; hg19: chr3-189580993;