7-87714706-T-C

Position:

• chr7-87714706-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001134405.2(RUNDC3B):​c.458+4051T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,376 control chromosomes in the GnomAD database, including 12,267 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 0.37 (12267 hom., cov: 30)
• Consequence: RUNDC3B NM_001134405.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

Genes affected

RUNDC3B (HGNC:30286): (RUN domain containing 3B)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RUNDC3B	NM_001134405.2	c.458+4051T>C		intron_variant		ENST00000394654.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RUNDC3B	ENST00000394654.4	c.458+4051T>C		intron_variant		2	NM_001134405.2	P1

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55865 AN: 151256 Hom.: 12276 Cov.: 30

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.369 AC: 55848 AN: 151376 Hom.: 12267 Cov.: 30 AF XY: 0.373 AC XY: 27582 AN XY: 73936

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.368

Alfa AF: 0.408 Hom.: 1680

Bravo AF: 0.353

Asia WGS AF: 0.517 AC: 1796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.11

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

Publications

LitVar

Other links and lift over

dbSNP: rs28656907; hg19: chr7-87344022;