Genetic Variant CIMIP1:p.Ile99Ile (chr20-58160705-C-T) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_178456.3(CIMIP1):c.297C>T(p.Ile99Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00393 in 1,614,132 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0028 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0041 ( 12 hom. )

Consequence

CIMIP1
NM_178456.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0850

Variant links:

Genes affected

CIMIP1 (HGNC:16216): (ciliary microtubule inner protein 1)

CIMIP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.24).

BP6

Variant 20-58160705-C-T is Benign according to our data. Variant chr20-58160705-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2652432.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.085 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 12 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIMIP1	NM_178456.3 link	c.297C>T	p.Ile99Ile	synonymous_variant	Exon 4 of 4	ENST00000371168.4	NP_848551.1	Q9H1P6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C20orf85	ENST00000371168.4 link	c.297C>T	p.Ile99Ile	synonymous_variant	Exon 4 of 4	1	NM_178456.3	ENSP00000360210.3		Q9H1P6

Frequencies

GnomAD3 genomes

AF:

0.00276

AC:

420

AN:

152244

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000820

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00288

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00486

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00249

AC:

625

AN:

251042

Hom.:

AF XY:

0.00252

AC XY:

342

AN XY:

135708

show subpopulations

Gnomad AFR exome

AF:

0.000866

Gnomad AMR exome

AF:

0.00226

Gnomad ASJ exome

AF:

0.000397

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000654

Gnomad FIN exome

AF:

0.000926

Gnomad NFE exome

AF:

0.00422

Gnomad OTH exome

AF:

0.00457

GnomAD4 exome

AF:

0.00405

AC:

5926

AN:

1461770

Hom.:

Cov.:

AF XY:

0.00395

AC XY:

2876

AN XY:

727188

show subpopulations

Gnomad4 AFR exome

AF:

0.000687

Gnomad4 AMR exome

AF:

0.00244

Gnomad4 ASJ exome

AF:

0.000268

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000928

Gnomad4 FIN exome

AF:

0.00116

Gnomad4 NFE exome

AF:

0.00494

Gnomad4 OTH exome

AF:

0.00361

GnomAD4 genome

AF:

0.00276

AC:

420

AN:

152362

Hom.:

Cov.:

AF XY:

0.00234

AC XY:

174

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.000818

Gnomad4 AMR

AF:

0.00287

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.000282

Gnomad4 NFE

AF:

0.00486

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00369

Hom.:

Bravo

AF:

0.00295

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00480

EpiControl

AF:

0.00474

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Mar 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CIMIP1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.24

CADD

Benign

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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