7-87787524-C-T

Variant names:

• chr7-87787524-C-T
• rs7793933
• NM_001134405.2:c.956+9569C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001134405.2(RUNDC3B):​c.956+9569C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 151,994 control chromosomes in the GnomAD database, including 33,362 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 0.64 (33362 hom., cov: 31)
• Consequence: RUNDC3B NM_001134405.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 3 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: Benign. The variant received -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 = 0.906 is higher than 0.05.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RUNDC3B	NM_001134405.2	MANE Select	c.956+9569C>T		intron	N/A	NP_001127877.1	Q96NL0-5
	RUNDC3B	NM_138290.3		c.1007+9569C>T		intron	N/A	NP_612147.1	Q96NL0-1
	RUNDC3B	NM_001394224.1		c.1007+9569C>T		intron	N/A	NP_001381153.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RUNDC3B	ENST00000394654.4	TSL:2 MANE Select	c.956+9569C>T		intron	N/A	ENSP00000378149.3	Q96NL0-5
	RUNDC3B	ENST00000493037.5	TSL:1	c.956+9569C>T		intron	N/A	ENSP00000420394.1	Q96NL0-4
	RUNDC3B	ENST00000338056.7	TSL:2	c.1007+9569C>T		intron	N/A	ENSP00000337732.3	Q96NL0-1

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96930 AN: 151876 Hom.: 33290 Cov.: 31

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.639 AC: 97072 AN: 151994 Hom.: 33362 Cov.: 31 AF XY: 0.634 AC XY: 47073 AN XY: 74264

African (AFR) AF: 0.913 AC: 37937 AN: 41530

American (AMR) AF: 0.600 AC: 9164 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3468

East Asian (EAS) AF: 0.533 AC: 2751 AN: 5166

South Asian (SAS) AF: 0.369 AC: 1772 AN: 4804

European-Finnish (FIN) AF: 0.549 AC: 5779 AN: 10524

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35665 AN: 67912

Other (OTH) AF: 0.638 AC: 1342 AN: 2104

Alfa AF: 0.593 Hom.: 3500

Bravo AF: 0.656

Asia WGS AF: 0.482 AC: 1681 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.8
DANN	Benign	0.43
PhyloP100		0.10
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7793933; hg19: chr7-87416839;