rs3092983

Variant names:

• chr15-40739577-G-A
• rs3092983
• NM_018145.3:c.971+556C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-40739577-G-A
• chr15-40739577-G-C
• chr15-40739577-G-T

Variant summary

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

The NM_018145.3(RMDN3):​c.971+556C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,716 control chromosomes in the GnomAD database, including 20,309 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 0.51 (20188 hom., cov: 31)
  • Exomes 𝑓: 0.51 (121 hom.)
• Consequence: RMDN3 NM_018145.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 7 publications found

Genes affected

RMDN3 (HGNC:25550): (regulator of microtubule dynamics 3) Enables microtubule binding activity. Involved in cellular calcium ion homeostasis. Located in several cellular components, including intercellular bridge; mitochondrial outer membrane; and spindle. [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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018145.3. 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
	RMDN3	NM_018145.3	MANE Select	c.971+556C>T		intron	N/A	NP_060615.1
	RMDN3	NM_001323896.2		c.1049+556C>T		intron	N/A	NP_001310825.1
	RMDN3	NM_001323897.2		c.1049+556C>T		intron	N/A	NP_001310826.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMDN3	ENST00000338376.8	TSL:1 MANE Select	c.971+556C>T		intron	N/A	ENSP00000342493.3
	RMDN3	ENST00000260385.10	TSL:1	c.971+556C>T		intron	N/A	ENSP00000260385.6
	RMDN3	ENST00000558777.5	TSL:2	n.*522+556C>T		intron	N/A	ENSP00000453357.1

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76870 AN: 151784 Hom.: 20169 Cov.: 31

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.500

GnomAD4 exome AF: 0.507 AC: 413 AN: 814 Hom.: 121 Cov.: 0 AF XY: 0.519 AC XY: 242 AN XY: 466

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.625 AC: 90 AN: 144

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AF: 0.929 AC: 13 AN: 14

South Asian (SAS) AF: 0.519 AC: 28 AN: 54

European-Finnish (FIN) AF: 0.625 AC: 5 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.471 AC: 260 AN: 552

Other (OTH) AF: 0.421 AC: 16 AN: 38

GnomAD4 genome AF: 0.506 AC: 76918 AN: 151902 Hom.: 20188 Cov.: 31 AF XY: 0.517 AC XY: 38361 AN XY: 74220

African (AFR) AF: 0.403 AC: 16696 AN: 41406

American (AMR) AF: 0.612 AC: 9335 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1965 AN: 3472

East Asian (EAS) AF: 0.794 AC: 4107 AN: 5170

South Asian (SAS) AF: 0.649 AC: 3120 AN: 4810

European-Finnish (FIN) AF: 0.586 AC: 6168 AN: 10526

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33892 AN: 67940

Other (OTH) AF: 0.504 AC: 1065 AN: 2112

Alfa AF: 0.490 Hom.: 4888

Bravo AF: 0.507

Asia WGS AF: 0.713 AC: 2479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	11
DANN	Benign	0.80
PhyloP100		0.29
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: rs3092983; hg19: chr15-41031775;