rs12704370

Variant names:

• chr7-87801354-G-A
• rs12704370
• NM_001134405.2:c.957-6019G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-87801354-G-A
• chr7-87801354-G-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.957-6019G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,050 control chromosomes in the GnomAD database, including 31,793 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 0.63 (31793 hom., cov: 32)
• Consequence: RUNDC3B NM_001134405.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 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.957-6019G>A		intron	N/A	NP_001127877.1	Q96NL0-5
	RUNDC3B	NM_138290.3		c.1008-6019G>A		intron	N/A	NP_612147.1	Q96NL0-1
	RUNDC3B	NM_001394224.1		c.1008-6019G>A		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.957-6019G>A		intron	N/A	ENSP00000378149.3	Q96NL0-5
	RUNDC3B	ENST00000493037.5	TSL:1	c.957-14787G>A		intron	N/A	ENSP00000420394.1	Q96NL0-4
	RUNDC3B	ENST00000338056.7	TSL:2	c.1008-6019G>A		intron	N/A	ENSP00000337732.3	Q96NL0-1

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95124 AN: 151932 Hom.: 31727 Cov.: 32

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.626 AC: 95259 AN: 152050 Hom.: 31793 Cov.: 32 AF XY: 0.622 AC XY: 46234 AN XY: 74326

African (AFR) AF: 0.877 AC: 36394 AN: 41516

American (AMR) AF: 0.596 AC: 9105 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1963 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2751 AN: 5180

South Asian (SAS) AF: 0.369 AC: 1774 AN: 4810

European-Finnish (FIN) AF: 0.547 AC: 5780 AN: 10568

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.523 AC: 35522 AN: 67914

Other (OTH) AF: 0.625 AC: 1321 AN: 2112

Alfa AF: 0.563 Hom.: 38068

Bravo AF: 0.643

Asia WGS AF: 0.480 AC: 1671 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	1.3
DANN	Benign	0.46
PhyloP100		0.059
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: rs12704370; hg19: chr7-87430669;