7-87825840-C-T

Position:

• chr7-87825840-C-T

Variant summary

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

The NM_001134405.2(RUNDC3B):​c.1226-4045C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,136 control chromosomes in the GnomAD database, including 33,253 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 (33253 hom., cov: 32)
• Consequence: RUNDC3B NM_001134405.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

Genes affected

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

RUNDC3B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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/exons	MANE	Protein	UniProt
RUNDC3B	NM_001134405.2	c.1226-4045C>T		intron_variant		ENST00000394654.4	NP_001127877.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RUNDC3B	ENST00000394654.4	c.1226-4045C>T		intron_variant		2	NM_001134405.2	ENSP00000378149.3
RUNDC3B	ENST00000493037.5	c.1079-4045C>T		intron_variant		1		ENSP00000420394.1
RUNDC3B	ENST00000338056.7	c.1277-4045C>T		intron_variant		2		ENSP00000337732.3
RUNDC3B	ENST00000312373.12	n.846-4045C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96811 AN: 152018 Hom.: 33182 Cov.: 32

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.637 AC: 96955 AN: 152136 Hom.: 33253 Cov.: 32 AF XY: 0.633 AC XY: 47057 AN XY: 74368

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.633

Alfa AF: 0.590 Hom.: 3476

Bravo AF: 0.655

Asia WGS AF: 0.499 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.44

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: rs6966166; hg19: chr7-87455155;