rs12704370

Positions:

• chr7-87801354-G-A
• chr7-87801354-G-C

Variant summary

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

The NM_001134405.2(RUNDC3B):​c.957-6019G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,050 control chromosomes in the GnomAD database, including 31,793 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 (31793 hom., cov: 32)
• Consequence: RUNDC3B NM_001134405.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

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=-1.0).
• 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	Protein	UniProt
RUNDC3B	NM_001134405.2	c.957-6019G>A		intron_variant		ENST00000394654.4	NP_001127877.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RUNDC3B	ENST00000394654.4	c.957-6019G>A		intron_variant		2	NM_001134405.2	ENSP00000378149	P1
RUNDC3B	ENST00000493037.5	c.957-14787G>A		intron_variant		1		ENSP00000420394
RUNDC3B	ENST00000338056.7	c.1008-6019G>A		intron_variant		2		ENSP00000337732
RUNDC3B	ENST00000312373.12	n.724-14787G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95124 AN: 151932 Hom.: 31727 Cov.: 32

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.626 AC: 95259 AN: 152050 Hom.: 31793 Cov.: 32 AF XY: 0.622 AC XY: 46234 AN XY: 74326

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.625

Alfa AF: 0.552 Hom.: 25070

Bravo AF: 0.643

Asia WGS AF: 0.480 AC: 1671 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	1.3
DANN	Benign	0.46

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: rs12704370; hg19: chr7-87430669;