7-87789546-T-C

Variant names:

• chr7-87789546-T-C
• rs1029421
• NM_001134405.2:c.956+11591T>C

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+11591T>C 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 152,052 control chromosomes in the GnomAD database, including 33,440 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 (33440 hom., cov: 31)
• Consequence: RUNDC3B NM_001134405.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RUNDC3B	NM_001134405.2	c.956+11591T>C		intron_variant	Intron 8 of 10	ENST00000394654.4	NP_001127877.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RUNDC3B	ENST00000394654.4	c.956+11591T>C		intron_variant	Intron 8 of 10	2	NM_001134405.2	ENSP00000378149.3
RUNDC3B	ENST00000493037.5	c.956+11591T>C		intron_variant	Intron 8 of 9	1		ENSP00000420394.1
RUNDC3B	ENST00000338056.7	c.1007+11591T>C		intron_variant	Intron 9 of 11	2		ENSP00000337732.3
RUNDC3B	ENST00000312373.12	n.723+11591T>C		intron_variant	Intron 6 of 7	5

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97070 AN: 151934 Hom.: 33368 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.526

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: 97213 AN: 152052 Hom.: 33440 Cov.: 31 AF XY: 0.634 AC XY: 47131 AN XY: 74292

African (AFR) AF: 0.914 AC: 37944 AN: 41520

American (AMR) AF: 0.600 AC: 9161 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2016 AN: 3470

East Asian (EAS) AF: 0.543 AC: 2810 AN: 5176

South Asian (SAS) AF: 0.369 AC: 1779 AN: 4818

European-Finnish (FIN) AF: 0.547 AC: 5763 AN: 10528

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35746 AN: 67964

Other (OTH) AF: 0.637 AC: 1343 AN: 2108

Alfa AF: 0.554 Hom.: 90306

Bravo AF: 0.658

Asia WGS AF: 0.486 AC: 1694 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.65
PhyloP100		-0.36
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: rs1029421; hg19: chr7-87418861;