Variant chr7-96039352-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001135556.2(DYNC1I1):c.1440C>A(p.Gly480Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 1,613,652 control chromosomes in the GnomAD database, including 36,881 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 3818 hom., cov: 33)

Exomes 𝑓: 0.21 ( 33063 hom. )

Consequence

DYNC1I1
NM_001135556.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.04

Variant links:

Genes affected

DYNC1I1 (HGNC:2963): (dynein cytoplasmic 1 intermediate chain 1) Enables spectrin binding activity. Involved in vesicle transport along microtubule. Located in several cellular components, including kinetochore; recycling endosome; and spindle pole. [provided by Alliance of Genome Resources, Apr 2022]

DYNC1I1 links:

DYNC1I1 (HGNC:):

DYNC1I1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 7-96039352-C-A is Benign according to our data. Variant chr7-96039352-C-A is described in ClinVar as [Benign]. Clinvar id is 402811.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.04 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DYNC1I1	NM_001135556.2 linkuse as main transcript	c.1440C>A	p.Gly480Gly	synonymous_variant	14/17	ENST00000447467.6	NP_001129028.1	O14576-2A4D1I7Q8N542

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DYNC1I1	ENST00000447467.6 linkuse as main transcript	c.1440C>A	p.Gly480Gly	synonymous_variant	14/17	1	NM_001135556.2	ENSP00000392337.2		O14576-2

Frequencies

GnomAD3 genomes

AF:

0.220

AC:

33487

AN:

152040

Hom.:

3818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.286

Gnomad EAS

AF:

0.315

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.186

Gnomad MID

AF:

0.220

Gnomad NFE

AF:

0.214

Gnomad OTH

AF:

0.241

GnomAD3 exomes

AF:

0.199

AC:

49833

AN:

250910

Hom.:

5467

AF XY:

0.195

AC XY:

26453

AN XY:

135636

show subpopulations

Gnomad AFR exome

AF:

0.230

Gnomad AMR exome

AF:

0.147

Gnomad ASJ exome

AF:

0.288

Gnomad EAS exome

AF:

0.310

Gnomad SAS exome

AF:

0.0912

Gnomad FIN exome

AF:

0.180

Gnomad NFE exome

AF:

0.215

Gnomad OTH exome

AF:

0.221

GnomAD4 exome

AF:

0.208

AC:

303451

AN:

1461494

Hom.:

33063

Cov.:

AF XY:

0.204

AC XY:

148371

AN XY:

727054

show subpopulations

Gnomad4 AFR exome

AF:

0.240

Gnomad4 AMR exome

AF:

0.156

Gnomad4 ASJ exome

AF:

0.286

Gnomad4 EAS exome

AF:

0.297

Gnomad4 SAS exome

AF:

0.0903

Gnomad4 FIN exome

AF:

0.182

Gnomad4 NFE exome

AF:

0.214

Gnomad4 OTH exome

AF:

0.208

GnomAD4 genome

AF:

0.220

AC:

33492

AN:

152158

Hom.:

3818

Cov.:

AF XY:

0.218

AC XY:

16208

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.233

Gnomad4 AMR

AF:

0.210

Gnomad4 ASJ

AF:

0.286

Gnomad4 EAS

AF:

0.315

Gnomad4 SAS

AF:

0.102

Gnomad4 FIN

AF:

0.186

Gnomad4 NFE

AF:

0.214

Gnomad4 OTH

AF:

0.239

Alfa

AF:

0.220

Hom.:

2195

Bravo

AF:

0.227

Asia WGS

AF:

0.195

AC:

680

AN:

3478

EpiCase

AF:

0.221

EpiControl

AF:

0.225

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

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 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

3.4

DANN

Benign

0.59

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