Variant chr7-158856569-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018051.5(DYNC2I1):c.-167C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 658,214 control chromosomes in the GnomAD database, including 9,930 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1925 hom., cov: 34)

Exomes 𝑓: 0.17 ( 8005 hom. )

Consequence

DYNC2I1
NM_018051.5 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.185

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:

LOC124901796 (HGNC:):

LOC124901796 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 7-158856569-C-T is Benign according to our data. Variant chr7-158856569-C-T is described in ClinVar as [Benign]. Clinvar id is 1250932.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.183 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.-167C>T		5_prime_UTR_variant	1/25	ENST00000407559.8	NP_060521.4
LOC124901796	XR_007060627.1 linkuse as main transcript			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DYNC2I1	ENST00000407559.8 linkuse as main transcript	c.-167C>T		5_prime_UTR_variant	1/25	1	NM_018051.5	ENSP00000384290	P1

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

23118

AN:

152126

Hom.:

1920

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.153

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.0523

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.181

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.186

Gnomad OTH

AF:

0.152

GnomAD4 exome

AF:

0.175

AC:

88519

AN:

505970

Hom.:

8005

Cov.:

AF XY:

0.174

AC XY:

43111

AN XY:

247598

show subpopulations

Gnomad4 AFR exome

AF:

0.111

Gnomad4 AMR exome

AF:

0.100

Gnomad4 ASJ exome

AF:

0.149

Gnomad4 EAS exome

AF:

0.0636

Gnomad4 SAS exome

AF:

0.196

Gnomad4 FIN exome

AF:

0.188

Gnomad4 NFE exome

AF:

0.186

Gnomad4 OTH exome

AF:

0.155

GnomAD4 genome

AF:

0.152

AC:

23126

AN:

152244

Hom.:

1925

Cov.:

AF XY:

0.151

AC XY:

11239

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.112

Gnomad4 AMR

AF:

0.108

Gnomad4 ASJ

AF:

0.154

Gnomad4 EAS

AF:

0.0524

Gnomad4 SAS

AF:

0.188

Gnomad4 FIN

AF:

0.181

Gnomad4 NFE

AF:

0.186

Gnomad4 OTH

AF:

0.149

Alfa

AF:

0.126

Hom.:

317

Bravo

AF:

0.142

Asia WGS

AF:

0.107

AC:

374

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.4

DANN

Benign

0.70

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