Variant chr7-95813378-T-TAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001135556.2(DYNC1I1):c.314+55_314+56dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.20 ( 3163 hom., cov: 0)

Exomes 𝑓: 0.14 ( 582 hom. )

Consequence

DYNC1I1
NM_001135556.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.299

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 7-95813378-T-TAA is Benign according to our data. Variant chr7-95813378-T-TAA is described in ClinVar as [Benign]. Clinvar id is 1283591.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DYNC1I1	NM_001135556.2 linkuse as main transcript	c.314+55_314+56dup		intron_variant		ENST00000447467.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYNC1I1	ENST00000447467.6 linkuse as main transcript	c.314+55_314+56dup		intron_variant		1	NM_001135556.2	P3	O14576-2

Frequencies

GnomAD3 genomes

AF:

0.198

AC:

27937

AN:

140896

Hom.:

3152

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.0343

Gnomad AMR

AF:

0.302

Gnomad ASJ

AF:

0.130

Gnomad EAS

AF:

0.423

Gnomad SAS

AF:

0.243

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.107

Gnomad NFE

AF:

0.145

Gnomad OTH

AF:

0.185

GnomAD4 exome

AF:

0.135

AC:

167571

AN:

1239034

Hom.:

582

Cov.:

AF XY:

0.135

AC XY:

82639

AN XY:

613684

show subpopulations

Gnomad4 AFR exome

AF:

0.204

Gnomad4 AMR exome

AF:

0.232

Gnomad4 ASJ exome

AF:

0.106

Gnomad4 EAS exome

AF:

0.266

Gnomad4 SAS exome

AF:

0.155

Gnomad4 FIN exome

AF:

0.108

Gnomad4 NFE exome

AF:

0.127

Gnomad4 OTH exome

AF:

0.141

GnomAD4 genome

AF:

0.198

AC:

27962

AN:

140906

Hom.:

3163

Cov.:

AF XY:

0.204

AC XY:

13896

AN XY:

68024

show subpopulations

Gnomad4 AFR

AF:

0.239

Gnomad4 AMR

AF:

0.303

Gnomad4 ASJ

AF:

0.130

Gnomad4 EAS

AF:

0.422

Gnomad4 SAS

AF:

0.243

Gnomad4 FIN

AF:

0.146

Gnomad4 NFE

AF:

0.145

Gnomad4 OTH

AF:

0.191

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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