Variant chr7-158869820-T-TTTTAAAC details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_018051.5(DYNC2I1):c.16-34_16-28dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 1,534,568 control chromosomes in the GnomAD database, including 110,783 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.45 ( 17132 hom., cov: 0)

Exomes 𝑓: 0.36 ( 93651 hom. )

Consequence

DYNC2I1
NM_018051.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.553

Variant links:

Genes affected

DYNC2I1 (HGNC:21862): (dynein 2 intermediate chain 1) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD) and may facilitate the formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes including cell cycle progression, signal transduction, apoptosis, and gene regulation. The encoded protein contains four WD repeats and may play a role in the formation of cilia. Mutations in this gene have been associated with short-rib polydactyly and Jeune syndromes. [provided by RefSeq, Mar 2014]

DYNC2I1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 7-158869820-T-TTTTAAAC is Benign according to our data. Variant chr7-158869820-T-TTTTAAAC is described in ClinVar as [Benign]. Clinvar id is 1266963.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DYNC2I1	NM_018051.5 linkuse as main transcript	c.16-34_16-28dup		intron_variant		ENST00000407559.8	NP_060521.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DYNC2I1	ENST00000407559.8 linkuse as main transcript	c.16-34_16-28dup		intron_variant		1	NM_018051.5	ENSP00000384290	P1
DYNC2I1	ENST00000397143.3 linkuse as main transcript	c.-123-34_-123-28dup		intron_variant		3		ENSP00000380330

Frequencies

GnomAD3 genomes

AF:

0.452

AC:

68457

AN:

151328

Hom.:

17091

Cov.:

show subpopulations

Gnomad AFR

AF:

0.667

Gnomad AMI

AF:

0.361

Gnomad AMR

AF:

0.402

Gnomad ASJ

AF:

0.338

Gnomad EAS

AF:

0.685

Gnomad SAS

AF:

0.474

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.451

Gnomad NFE

AF:

0.338

Gnomad OTH

AF:

0.427

GnomAD3 exomes

AF:

0.388

AC:

85291

AN:

219840

Hom.:

17776

AF XY:

0.387

AC XY:

46376

AN XY:

119980

show subpopulations

Gnomad AFR exome

AF:

0.661

Gnomad AMR exome

AF:

0.347

Gnomad ASJ exome

AF:

0.326

Gnomad EAS exome

AF:

0.660

Gnomad SAS exome

AF:

0.450

Gnomad FIN exome

AF:

0.341

Gnomad NFE exome

AF:

0.323

Gnomad OTH exome

AF:

0.365

GnomAD4 exome

AF:

0.356

AC:

492645

AN:

1383118

Hom.:

93651

Cov.:

AF XY:

0.358

AC XY:

247509

AN XY:

690688

show subpopulations

Gnomad4 AFR exome

AF:

0.674

Gnomad4 AMR exome

AF:

0.357

Gnomad4 ASJ exome

AF:

0.335

Gnomad4 EAS exome

AF:

0.669

Gnomad4 SAS exome

AF:

0.456

Gnomad4 FIN exome

AF:

0.350

Gnomad4 NFE exome

AF:

0.328

Gnomad4 OTH exome

AF:

0.374

GnomAD4 genome

AF:

0.453

AC:

68554

AN:

151450

Hom.:

17132

Cov.:

AF XY:

0.457

AC XY:

33787

AN XY:

73972

show subpopulations

Gnomad4 AFR

AF:

0.668

Gnomad4 AMR

AF:

0.402

Gnomad4 ASJ

AF:

0.338

Gnomad4 EAS

AF:

0.685

Gnomad4 SAS

AF:

0.477

Gnomad4 FIN

AF:

0.349

Gnomad4 NFE

AF:

0.338

Gnomad4 OTH

AF:

0.427

Alfa

AF:

0.386

Hom.:

1975

Asia WGS

AF:

0.551

AC:

1916

AN:

3478

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

Nov 12, 2018

- -

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