chr7-87714706-T-C

Variant names:

• chr7-87714706-T-C
• rs28656907
• NM_001134405.2:c.458+4051T>C

Variant summary

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

The NM_138290.3(RUNDC3B):​c.509+4051T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,376 control chromosomes in the GnomAD database, including 12,267 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 0.37 (12267 hom., cov: 30)
• Consequence: RUNDC3B NM_138290.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 8 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=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138290.3. 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+4051T>C		intron	N/A	NP_001127877.1
	RUNDC3B	NM_138290.3		c.509+4051T>C		intron	N/A	NP_612147.1
	RUNDC3B	NM_001394224.1		c.509+4051T>C		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+4051T>C		intron	N/A	ENSP00000378149.3
	RUNDC3B	ENST00000493037.5	TSL:1	c.458+4051T>C		intron	N/A	ENSP00000420394.1
	RUNDC3B	ENST00000338056.7	TSL:2	c.509+4051T>C		intron	N/A	ENSP00000337732.3

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55865 AN: 151256 Hom.: 12276 Cov.: 30

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.369 AC: 55848 AN: 151376 Hom.: 12267 Cov.: 30 AF XY: 0.373 AC XY: 27582 AN XY: 73936

African (AFR) AF: 0.114 AC: 4732 AN: 41382

American (AMR) AF: 0.401 AC: 6106 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1449 AN: 3464

East Asian (EAS) AF: 0.465 AC: 2370 AN: 5098

South Asian (SAS) AF: 0.632 AC: 3038 AN: 4810

European-Finnish (FIN) AF: 0.452 AC: 4722 AN: 10454

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.475 AC: 32102 AN: 67654

Other (OTH) AF: 0.368 AC: 775 AN: 2106

Alfa AF: 0.408 Hom.: 1680

Bravo AF: 0.353

Asia WGS AF: 0.517 AC: 1796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.11
PhyloP100		-1.6
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: rs28656907; hg19: chr7-87344022;