chr7-87773220-A-G

Position:

• chr7-87773220-A-G

Variant summary

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

The NM_001134405.2(RUNDC3B):​c.798+2471A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 151,340 control chromosomes in the GnomAD database, including 31,791 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 0.63 (31791 hom., cov: 28)
• Consequence: RUNDC3B NM_001134405.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RUNDC3B	NM_001134405.2	c.798+2471A>G		intron_variant		ENST00000394654.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RUNDC3B	ENST00000394654.4	c.798+2471A>G		intron_variant		2	NM_001134405.2	P1
RUNDC3B	ENST00000493037.5	c.798+2471A>G		intron_variant		1
RUNDC3B	ENST00000338056.7	c.849+2471A>G		intron_variant		2
RUNDC3B	ENST00000312373.12	n.565+2471A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.628 AC: 94941 AN: 151220 Hom.: 31725 Cov.: 28

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.628 AC: 95077 AN: 151340 Hom.: 31791 Cov.: 28 AF XY: 0.624 AC XY: 46129 AN XY: 73946

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.629

Alfa AF: 0.584 Hom.: 3310

Bravo AF: 0.645

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.57

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: rs6465119; hg19: chr7-87402536;