chr1-171831196-T-C

Variant names:

• chr1-171831196-T-C
• rs764180
• ENST00000688173.1:c.-96+13153T>C

Variant summary

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

The ENST00000688173.1(DNM3):​c.-96+13153T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,082 control chromosomes in the GnomAD database, including 17,359 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 0.47 (17359 hom., cov: 33)
• Consequence: DNM3 ENST00000688173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNM3	ENST00000688173.1	c.-96+13153T>C		intron_variant	Intron 1 of 14			ENSP00000509172.1

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72009 AN: 151966 Hom.: 17344 Cov.: 33

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.474 AC: 72052 AN: 152082 Hom.: 17359 Cov.: 33 AF XY: 0.472 AC XY: 35062 AN XY: 74348

African (AFR) AF: 0.521 AC: 21588 AN: 41456

American (AMR) AF: 0.428 AC: 6549 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1800 AN: 3468

East Asian (EAS) AF: 0.643 AC: 3327 AN: 5176

South Asian (SAS) AF: 0.311 AC: 1499 AN: 4822

European-Finnish (FIN) AF: 0.432 AC: 4568 AN: 10572

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31205 AN: 67998

Other (OTH) AF: 0.469 AC: 987 AN: 2104

Alfa AF: 0.466 Hom.: 3516

Bravo AF: 0.475

Asia WGS AF: 0.485 AC: 1690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	8.6
DANN	Benign	0.76
PhyloP100		0.097

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs764180; hg19: chr1-171800336;