rs9472494

Positions:

• chr6-45484099-C-T

Variant summary

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

The NM_001024630.4(RUNX2):​c.686-7842C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 151,968 control chromosomes in the GnomAD database, including 7,462 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 0.31 (7462 hom., cov: 32)
• Consequence: RUNX2 NM_001024630.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

RUNX2 (HGNC:10472): (RUNX family transcription factor 2) This gene is a member of the RUNX family of transcription factors and encodes a nuclear protein with an Runt DNA-binding domain. This protein is essential for osteoblastic differentiation and skeletal morphogenesis and acts as a scaffold for nucleic acids and regulatory factors involved in skeletal gene expression. The protein can bind DNA both as a monomer or, with more affinity, as a subunit of a heterodimeric complex. Two regions of potential trinucleotide repeat expansions are present in the N-terminal region of the encoded protein, and these and other mutations in this gene have been associated with the bone development disorder cleidocranial dysplasia (CCD). Transcript variants that encode different protein isoforms result from the use of alternate promoters as well as alternate splicing. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RUNX2	NM_001024630.4	c.686-7842C>T		intron_variant		ENST00000647337.2
RUNX2	NM_001015051.4	c.686-7842C>T		intron_variant
RUNX2	NM_001278478.2	c.644-7842C>T		intron_variant
RUNX2	NM_001369405.1	c.644-7842C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RUNX2	ENST00000647337.2	c.686-7842C>T		intron_variant			NM_001024630.4	P4

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46744 AN: 151850 Hom.: 7459 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.0502

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.308 AC: 46762 AN: 151968 Hom.: 7462 Cov.: 32 AF XY: 0.305 AC XY: 22655 AN XY: 74254

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.0495

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.296

Alfa AF: 0.335 Hom.: 8267

Bravo AF: 0.305

Asia WGS AF: 0.168 AC: 586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.72

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: rs9472494; hg19: chr6-45451836;