chr7-87787524-C-T

Variant names:

• chr7-87787524-C-T
• rs7793933
• NM_001134405.2:c.956+9569C>T

Variant summary

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

The NM_001134405.2(RUNDC3B):​c.956+9569C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 151,994 control chromosomes in the GnomAD database, including 33,362 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 0.64 (33362 hom., cov: 31)
• Consequence: RUNDC3B NM_001134405.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RUNDC3B	NM_001134405.2	c.956+9569C>T		intron_variant	Intron 8 of 10	ENST00000394654.4	NP_001127877.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RUNDC3B	ENST00000394654.4	c.956+9569C>T		intron_variant	Intron 8 of 10	2	NM_001134405.2	ENSP00000378149.3
RUNDC3B	ENST00000493037.5	c.956+9569C>T		intron_variant	Intron 8 of 9	1		ENSP00000420394.1
RUNDC3B	ENST00000338056.7	c.1007+9569C>T		intron_variant	Intron 9 of 11	2		ENSP00000337732.3
RUNDC3B	ENST00000312373.12	n.723+9569C>T		intron_variant	Intron 6 of 7	5

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96930 AN: 151876 Hom.: 33290 Cov.: 31

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.639 AC: 97072 AN: 151994 Hom.: 33362 Cov.: 31 AF XY: 0.634 AC XY: 47073 AN XY: 74264

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.638

Alfa AF: 0.580 Hom.: 3196

Bravo AF: 0.656

Asia WGS AF: 0.482 AC: 1681 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.8
DANN	Benign	0.43

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: rs7793933; hg19: chr7-87416839;