NM_015569.5:c.236-17506C>A

Variant names:

• chr1-171970150-C-A
• rs2038479
• NM_015569.5:c.236-17506C>A

Variant summary

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

The NM_015569.5(DNM3):​c.236-17506C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 509,006 control chromosomes in the GnomAD database, including 153,316 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 0.81 (49510 hom., cov: 31)
  • Exomes 𝑓: 0.76 (103806 hom.)
• Consequence: DNM3 NM_015569.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594
• Publications: 8 publications found

Genes affected

DNM3 (HGNC:29125): (dynamin 3) This gene encodes a member of a family of guanosine triphosphate (GTP)-binding proteins that associate with microtubules and are involved in vesicular transport. The encoded protein functions in the development of megakaryocytes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNM3	NM_015569.5	c.236-17506C>A		intron_variant	Intron 2 of 20	ENST00000627582.3	NP_056384.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNM3	ENST00000627582.3	c.236-17506C>A		intron_variant	Intron 2 of 20	1	NM_015569.5	ENSP00000486701.1

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122607 AN: 151954 Hom.: 49462 Cov.: 31

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.822

GnomAD4 exome AF: 0.762 AC: 271864 AN: 356938 Hom.: 103806 Cov.: 2 AF XY: 0.764 AC XY: 128658 AN XY: 168506

African (AFR) AF: 0.786 AC: 5363 AN: 6826

American (AMR) AF: 0.724 AC: 275 AN: 380

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 1818 AN: 2218

East Asian (EAS) AF: 0.708 AC: 1118 AN: 1578

South Asian (SAS) AF: 0.775 AC: 5266 AN: 6794

European-Finnish (FIN) AF: 0.611 AC: 77 AN: 126

Middle Eastern (MID) AF: 0.815 AC: 572 AN: 702

European-Non Finnish (NFE) AF: 0.761 AC: 248633 AN: 326886

Other (OTH) AF: 0.765 AC: 8742 AN: 11428

GnomAD4 genome AF: 0.807 AC: 122714 AN: 152068 Hom.: 49510 Cov.: 31 AF XY: 0.805 AC XY: 59789 AN XY: 74308

African (AFR) AF: 0.818 AC: 33954 AN: 41490

American (AMR) AF: 0.803 AC: 12250 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2968 AN: 3472

East Asian (EAS) AF: 0.761 AC: 3943 AN: 5184

South Asian (SAS) AF: 0.808 AC: 3888 AN: 4814

European-Finnish (FIN) AF: 0.786 AC: 8305 AN: 10560

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54655 AN: 67974

Other (OTH) AF: 0.825 AC: 1739 AN: 2108

Alfa AF: 0.807 Hom.: 79711

Bravo AF: 0.811

Asia WGS AF: 0.803 AC: 2788 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.75
PhyloP100		0.59
PromoterAI		-0.042	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs2038479; hg19: chr1-171939290;