7-87717503-G-T

Variant names:

• chr7-87717503-G-T
• rs17160359
• NM_001134405.2:c.458+6848G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001134405.2(RUNDC3B):​c.458+6848G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00399 in 152,010 control chromosomes in the GnomAD database, including 8 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 0.0040 (8 hom., cov: 32)
• Consequence: RUNDC3B NM_001134405.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.978
• Publications: 4 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=-0.87).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00399 (607/152010) while in subpopulation EAS AF = 0.0494 (256/5180). AF 95% confidence interval is 0.0445. There are 8 homozygotes in GnomAd4. There are 379 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 8 Unknown gene

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+6848G>T		intron	N/A	NP_001127877.1
	RUNDC3B	NM_138290.3		c.509+6848G>T		intron	N/A	NP_612147.1
	RUNDC3B	NM_001394224.1		c.509+6848G>T		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+6848G>T		intron	N/A	ENSP00000378149.3
	RUNDC3B	ENST00000493037.5	TSL:1	c.458+6848G>T		intron	N/A	ENSP00000420394.1
	RUNDC3B	ENST00000338056.7	TSL:2	c.509+6848G>T		intron	N/A	ENSP00000337732.3

Frequencies

GnomAD3 genomes AF: 0.00400 AC: 607 AN: 151892 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.000338

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0108

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0493

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000412

Gnomad OTH AF: 0.00192

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

GnomAD4 genome AF: 0.00399 AC: 607 AN: 152010 Hom.: 8 Cov.: 32 AF XY: 0.00510 AC XY: 379 AN XY: 74308

African (AFR) AF: 0.000337 AC: 14 AN: 41516

American (AMR) AF: 0.0108 AC: 164 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.0494 AC: 256 AN: 5180

South Asian (SAS) AF: 0.00228 AC: 11 AN: 4830

European-Finnish (FIN) AF: 0.0123 AC: 129 AN: 10512

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000412 AC: 28 AN: 67938

Other (OTH) AF: 0.00237 AC: 5 AN: 2110

Alfa AF: 0.000669 Hom.: 0

Bravo AF: 0.00538

Asia WGS AF: 0.0200 AC: 70 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.0
DANN	Benign	0.71
PhyloP100		0.98
Mutation Taster		=100/0	polymorphism

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: rs17160359; hg19: chr7-87346819;