7-87714706-TG-CC

Variant names:

• chr7-87714706-TG-CC
• rs35901799
• NM_001134405.2:c.458+4051_458+4052delTGinsCC

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001134405.2(RUNDC3B):​c.458+4051_458+4052delTGinsCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 30)
• Consequence: RUNDC3B NM_001134405.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 1 publications found

Genes affected

RUNDC3B (HGNC:30286): (RUN domain containing 3B)

RUNDC3B Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001134405.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RUNDC3B	NM_001134405.2	MANE Select	c.458+4051_458+4052delTGinsCC		intron	N/A	NP_001127877.1
	RUNDC3B	NM_138290.3		c.509+4051_509+4052delTGinsCC		intron	N/A	NP_612147.1
	RUNDC3B	NM_001394224.1		c.509+4051_509+4052delTGinsCC		intron	N/A	NP_001381153.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RUNDC3B	ENST00000394654.4	TSL:2 MANE Select	c.458+4051_458+4052delTGinsCC		intron	N/A	ENSP00000378149.3
	RUNDC3B	ENST00000493037.5	TSL:1	c.458+4051_458+4052delTGinsCC		intron	N/A	ENSP00000420394.1
	RUNDC3B	ENST00000338056.7	TSL:2	c.509+4051_509+4052delTGinsCC		intron	N/A	ENSP00000337732.3

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs35901799; hg19: chr7-87344022;