Variant 7-95827848-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001135556.2(DYNC1I1):c.315-209C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,858 control chromosomes in the GnomAD database, including 21,416 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.52 ( 21416 hom., cov: 31)

Consequence

DYNC1I1
NM_001135556.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.310

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 7-95827848-C-T is Benign according to our data. Variant chr7-95827848-C-T is described in ClinVar as [Benign]. Clinvar id is 1294648.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 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.315-209C>T		intron_variant		ENST00000447467.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYNC1I1	ENST00000447467.6 linkuse as main transcript	c.315-209C>T		intron_variant		1	NM_001135556.2	P3	O14576-2

Frequencies

GnomAD3 genomes

AF:

0.521

AC:

79127

AN:

151740

Hom.:

21368

Cov.:

show subpopulations

Gnomad AFR

AF:

0.669

Gnomad AMI

AF:

0.495

Gnomad AMR

AF:

0.549

Gnomad ASJ

AF:

0.405

Gnomad EAS

AF:

0.581

Gnomad SAS

AF:

0.467

Gnomad FIN

AF:

0.474

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.439

Gnomad OTH

AF:

0.515

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.522

AC:

79241

AN:

151858

Hom.:

21416

Cov.:

AF XY:

0.523

AC XY:

38780

AN XY:

74178

show subpopulations

Gnomad4 AFR

AF:

0.669

Gnomad4 AMR

AF:

0.550

Gnomad4 ASJ

AF:

0.405

Gnomad4 EAS

AF:

0.581

Gnomad4 SAS

AF:

0.468

Gnomad4 FIN

AF:

0.474

Gnomad4 NFE

AF:

0.439

Gnomad4 OTH

AF:

0.523

Alfa

AF:

0.483

Hom.:

3021

Bravo

AF:

0.536

Asia WGS

AF:

0.577

AC:

2003

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

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.5

DANN

Benign

0.68

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