chr17-44316094-A-C

Variant names:

• chr17-44316094-A-C
• rs11654436
• NM_001144825.2:c.954-291A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001144825.2(RUNDC3A):​c.954-291A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,546 control chromosomes in the GnomAD database, including 24,086 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 0.54 (24086 hom., cov: 29)
• Consequence: RUNDC3A NM_001144825.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 8 publications found

Genes affected

RUNDC3A (HGNC:16984): (RUN domain containing 3A) Predicted to enable GTPase regulator activity. Predicted to be involved in positive regulation of cGMP-mediated signaling. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144825.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RUNDC3A	NM_001144825.2	MANE Select	c.954-291A>C		intron	N/A	NP_001138297.1
	RUNDC3A	NM_006695.5		c.954-291A>C		intron	N/A	NP_006686.1
	RUNDC3A	NM_001144826.2		c.939-291A>C		intron	N/A	NP_001138298.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RUNDC3A	ENST00000426726.8	TSL:1 MANE Select	c.954-291A>C		intron	N/A	ENSP00000410862.2
	RUNDC3A	ENST00000225441.11	TSL:1	c.954-291A>C		intron	N/A	ENSP00000225441.7
	RUNDC3A	ENST00000590941.5	TSL:1	c.939-291A>C		intron	N/A	ENSP00000468214.1

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81280 AN: 151428 Hom.: 24026 Cov.: 29

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.537 AC: 81406 AN: 151546 Hom.: 24086 Cov.: 29 AF XY: 0.547 AC XY: 40526 AN XY: 74032

African (AFR) AF: 0.749 AC: 30913 AN: 41260

American (AMR) AF: 0.560 AC: 8509 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1427 AN: 3468

East Asian (EAS) AF: 0.916 AC: 4710 AN: 5144

South Asian (SAS) AF: 0.650 AC: 3123 AN: 4802

European-Finnish (FIN) AF: 0.497 AC: 5229 AN: 10522

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25933 AN: 67834

Other (OTH) AF: 0.508 AC: 1071 AN: 2108

Alfa AF: 0.459 Hom.: 6791

Bravo AF: 0.554

Asia WGS AF: 0.790 AC: 2745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.2
DANN	Benign	0.74
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11654436; hg19: chr17-42393462;