dbSNP rs3821091: DYNC1I2:c.512-16T>G (chr2-171725602-T-G) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_001378.3(DYNC1I2):c.512-16T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.00058 ( 0 hom., cov: 16)

Exomes 𝑓: 0.0082 ( 6 hom. )

Consequence

DYNC1I2
NM_001378.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.429

Variant links:

Genes affected

DYNC1I2 (HGNC:2964): (dynein cytoplasmic 1 intermediate chain 2) This gene encodes a member of the dynein intermediate chain family. The encoded protein is a non-catalytic component of the cytoplasmic dynein 1 complex, which acts as a retrograde microtubule motor to transport organelles and vesicles. A pseudogene of this gene is located on chromosome 10. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

DYNC1I2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 2-171725602-T-G is Benign according to our data. Variant chr2-171725602-T-G is described in ClinVar as [Benign]. Clinvar id is 402814.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAdExome4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DYNC1I2	NM_001378.3 link	c.512-16T>G		intron_variant	Intron 7 of 17	ENST00000397119.8	NP_001369.1	Q13409-1A0A140VKE9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DYNC1I2	ENST00000397119.8 link	c.512-16T>G		intron_variant	Intron 7 of 17	1	NM_001378.3	ENSP00000380308.3		Q13409-1

Frequencies

GnomAD3 genomes

AF:

0.000573

AC:

AN:

80294

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000647

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000568

Gnomad ASJ

AF:

0.00498

Gnomad EAS

AF:

0.00117

Gnomad SAS

AF:

0.000303

Gnomad FIN

AF:

0.000169

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000369

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0248

AC:

1478

AN:

59630

Hom.:

AF XY:

0.0254

AC XY:

821

AN XY:

32372

show subpopulations

Gnomad AFR exome

AF:

0.0492

Gnomad AMR exome

AF:

0.0228

Gnomad ASJ exome

AF:

0.0232

Gnomad EAS exome

AF:

0.0276

Gnomad SAS exome

AF:

0.0125

Gnomad FIN exome

AF:

0.00849

Gnomad NFE exome

AF:

0.0327

Gnomad OTH exome

AF:

0.0255

GnomAD4 exome

AF:

0.00823

AC:

7297

AN:

886700

Hom.:

Cov.:

AF XY:

0.00848

AC XY:

3741

AN XY:

441232

show subpopulations

Gnomad4 AFR exome

AF:

0.0109

Gnomad4 AMR exome

AF:

0.00871

Gnomad4 ASJ exome

AF:

0.00954

Gnomad4 EAS exome

AF:

0.00497

Gnomad4 SAS exome

AF:

0.00639

Gnomad4 FIN exome

AF:

0.00393

Gnomad4 NFE exome

AF:

0.00866

Gnomad4 OTH exome

AF:

0.00740

GnomAD4 genome

AF:

0.000585

AC:

AN:

80374

Hom.:

Cov.:

AF XY:

0.000501

AC XY:

AN XY:

39894

show subpopulations

Gnomad4 AFR

AF:

0.000693

Gnomad4 AMR

AF:

0.000568

Gnomad4 ASJ

AF:

0.00498

Gnomad4 EAS

AF:

0.00117

Gnomad4 SAS

AF:

0.000304

Gnomad4 FIN

AF:

0.000169

Gnomad4 NFE

AF:

0.000369

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0144

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.29

DANN

Benign

0.38

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over