chr1-171970150-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_015569.5(DNM3):​c.236-17506C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 361056 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 170456

African (AFR) AF: 0.00 AC: 0 AN: 6904

American (AMR) AF: 0.00 AC: 0 AN: 386

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2232

East Asian (EAS) AF: 0.00 AC: 0 AN: 1606

South Asian (SAS) AF: 0.00 AC: 0 AN: 6858

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 126

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 710

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 330672

Other (OTH) AF: 0.00 AC: 0 AN: 11562

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 79711

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.63
PhyloP100		0.59
PromoterAI		-0.043	Neutral

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: rs2038479; hg19: chr1-171939290;