rs12944462

Positions:

• chr17-42985484-C-A
• chr17-42985484-C-G
• chr17-42985484-C-T

Variant summary

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

The ENST00000361677.6(RUNDC1):​c.499-1772C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,974 control chromosomes in the GnomAD database, including 29,645 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 0.60 (29645 hom., cov: 32)
• Consequence: RUNDC1 ENST00000361677.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.16

Genes affected

RUNDC1 (HGNC:25418): (RUN domain containing 1) This gene encodes a protein that contains a RUN (RPIP8, UNC-14 and NESCA) domain and a coiled coil domain. The encoded protein may negatively regulate p53 transcriptional activity. This gene is a potential candidate gene for predisposition to glioma in humans. [provided by RefSeq, May 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RUNDC1	NM_173079.5	c.499-1772C>A		intron_variant		ENST00000361677.6	NP_775102.3
RUNDC1	NM_001321381.3	c.499-167C>A		intron_variant			NP_001308310.2
RUNDC1	NM_001394222.1	c.499-1772C>A		intron_variant			NP_001381151.1
RUNDC1	XM_005257078.5	c.499-167C>A		intron_variant			XP_005257135.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RUNDC1	ENST00000361677.6	c.499-1772C>A		intron_variant		1	NM_173079.5	ENSP00000354622	P1
RUNDC1	ENST00000589705.1	c.495-1772C>A		intron_variant		5		ENSP00000467953

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90957 AN: 151856 Hom.: 29625 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.599 AC: 91008 AN: 151974 Hom.: 29645 Cov.: 32 AF XY: 0.602 AC XY: 44741 AN XY: 74288

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.645

Alfa AF: 0.694 Hom.: 59309

Bravo AF: 0.594

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.046
DANN	Benign	0.35

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: rs12944462; hg19: chr17-41137501;