chr7-87745553-T-G

Variant names:

• chr7-87745553-T-G
• rs114137957
• NM_001134405.2:c.629+3974T>G

Variant summary

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

The NM_001134405.2(RUNDC3B):​c.629+3974T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0317 in 152,246 control chromosomes in the GnomAD database, including 134 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 0.032 (134 hom., cov: 32)
• Consequence: RUNDC3B NM_001134405.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416
• Publications: 1 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 = 0.0734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RUNDC3B	NM_001134405.2	c.629+3974T>G		intron_variant	Intron 6 of 10	ENST00000394654.4	NP_001127877.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RUNDC3B	ENST00000394654.4	c.629+3974T>G		intron_variant	Intron 6 of 10	2	NM_001134405.2	ENSP00000378149.3

Frequencies

GnomAD3 genomes AF: 0.0316 AC: 4804 AN: 152130 Hom.: 131 Cov.: 32

Gnomad AFR AF: 0.0755

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0104

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.0394

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0134

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0317 AC: 4823 AN: 152246 Hom.: 134 Cov.: 32 AF XY: 0.0318 AC XY: 2367 AN XY: 74442

African (AFR) AF: 0.0756 AC: 3144 AN: 41562

American (AMR) AF: 0.0104 AC: 159 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0207 AC: 72 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5192

South Asian (SAS) AF: 0.0135 AC: 65 AN: 4822

European-Finnish (FIN) AF: 0.0394 AC: 417 AN: 10594

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0134 AC: 912 AN: 67992

Other (OTH) AF: 0.0232 AC: 49 AN: 2114

Alfa AF: 0.0240 Hom.: 6

Bravo AF: 0.0316

Asia WGS AF: 0.0140 AC: 49 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.51
PhyloP100		0.42
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: rs114137957; hg19: chr7-87374869;