rs6908650

Positions:

• chr6-45390370-G-A

Variant summary

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

The NM_001024630.4(RUNX2):​c.59-32223G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 152,056 control chromosomes in the GnomAD database, including 13,498 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 0.42 (13498 hom., cov: 33)
• Consequence: RUNX2 NM_001024630.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.457

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RUNX2	NM_001024630.4	c.59-32223G>A		intron_variant		ENST00000647337.2
RUNX2	NM_001015051.4	c.59-32223G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RUNX2	ENST00000647337.2	c.59-32223G>A		intron_variant			NM_001024630.4	P4

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63441 AN: 151938 Hom.: 13481 Cov.: 33

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.417 AC: 63481 AN: 152056 Hom.: 13498 Cov.: 33 AF XY: 0.417 AC XY: 31003 AN XY: 74324

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.436

Alfa AF: 0.443 Hom.: 14417

Bravo AF: 0.405

Asia WGS AF: 0.418 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.69

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: rs6908650; hg19: chr6-45358107;