7-87816433-G-T

Variant names:

• chr7-87816433-G-T
• rs10235853
• NM_001134405.2:c.1225+171G>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.1225+171G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 151,298 control chromosomes in the GnomAD database, including 40,862 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 0.73 (40862 hom., cov: 29)
• Consequence: RUNDC3B NM_001134405.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.600
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RUNDC3B	NM_001134405.2	c.1225+171G>T		intron_variant	Intron 10 of 10	ENST00000394654.4	NP_001127877.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RUNDC3B	ENST00000394654.4	c.1225+171G>T		intron_variant	Intron 10 of 10	2	NM_001134405.2	ENSP00000378149.3
RUNDC3B	ENST00000493037.5	c.1078+171G>T		intron_variant	Intron 9 of 9	1		ENSP00000420394.1
RUNDC3B	ENST00000338056.7	c.1276+171G>T		intron_variant	Intron 11 of 11	2		ENSP00000337732.3
RUNDC3B	ENST00000312373.12	n.845+171G>T		intron_variant	Intron 7 of 7	5

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110087 AN: 151180 Hom.: 40792 Cov.: 29

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.729 AC: 110222 AN: 151298 Hom.: 40862 Cov.: 29 AF XY: 0.722 AC XY: 53396 AN XY: 73910

African (AFR) AF: 0.862 AC: 35574 AN: 41260

American (AMR) AF: 0.672 AC: 10186 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2789 AN: 3450

East Asian (EAS) AF: 0.472 AC: 2430 AN: 5152

South Asian (SAS) AF: 0.585 AC: 2797 AN: 4782

European-Finnish (FIN) AF: 0.664 AC: 6960 AN: 10478

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.695 AC: 47076 AN: 67720

Other (OTH) AF: 0.749 AC: 1575 AN: 2102

Alfa AF: 0.689 Hom.: 9420

Bravo AF: 0.736

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.50
DANN	Benign	0.18
PhyloP100		0.60
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: rs10235853; hg19: chr7-87445748; COSMIC: COSV56690752;