chr18-70020624-T-C

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_173630.4(RTTN):c.6144A>G(p.Val2048Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 1,612,234 control chromosomes in the GnomAD database, including 32,809 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2385 hom., cov: 32)

Exomes 𝑓: 0.20 ( 30424 hom. )

Consequence

RTTN
NM_173630.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.268

Variant links:

Genes affected

RTTN (HGNC:18654): (rotatin) This gene encodes a large protein whose specific function is unknown. Absence of the orthologous protein in mouse results in embryonic lethality with deficient axial rotation, abnormal differentiation of the neural tube, and randomized looping of the heart tube during development. In human, mutations in this gene are associated with polymicrogyria with seizures. In human fibroblasts this protein localizes at the ciliary basal bodies. Given the intracellular localization of this protein and the phenotypic effects of mutations, this gene is suspected of playing a role in the maintenance of normal ciliary structure which in turn effects the developmental process of left-right organ specification, axial rotation, and perhaps notochord development. [provided by RefSeq, Jan 2013]

RTTN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP6

Variant 18-70020624-T-C is Benign according to our data. Variant chr18-70020624-T-C is described in ClinVar as [Benign]. Clinvar id is 130191.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-70020624-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.268 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RTTN	NM_173630.4 link	c.6144A>G	p.Val2048Val	synonymous_variant	Exon 45 of 49	ENST00000640769.2	NP_775901.3	Q86VV8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RTTN	ENST00000640769.2 link	c.6144A>G	p.Val2048Val	synonymous_variant	Exon 45 of 49	2	NM_173630.4	ENSP00000491507.1		Q86VV8-1

Frequencies

GnomAD3 genomes

AF:

0.169

AC:

25642

AN:

152118

Hom.:

2389

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0867

Gnomad AMI

AF:

0.230

Gnomad AMR

AF:

0.156

Gnomad ASJ

AF:

0.246

Gnomad EAS

AF:

0.180

Gnomad SAS

AF:

0.215

Gnomad FIN

AF:

0.190

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.207

Gnomad OTH

AF:

0.213

GnomAD3 exomes

AF:

0.191

AC:

47546

AN:

248918

Hom.:

4854

AF XY:

0.200

AC XY:

27063

AN XY:

135026

show subpopulations

Gnomad AFR exome

AF:

0.0797

Gnomad AMR exome

AF:

0.110

Gnomad ASJ exome

AF:

0.256

Gnomad EAS exome

AF:

0.193

Gnomad SAS exome

AF:

0.230

Gnomad FIN exome

AF:

0.196

Gnomad NFE exome

AF:

0.212

Gnomad OTH exome

AF:

0.227

GnomAD4 exome

AF:

0.201

AC:

292984

AN:

1459998

Hom.:

30424

Cov.:

AF XY:

0.203

AC XY:

147590

AN XY:

726224

show subpopulations

Gnomad4 AFR exome

AF:

0.0906

Gnomad4 AMR exome

AF:

0.116

Gnomad4 ASJ exome

AF:

0.256

Gnomad4 EAS exome

AF:

0.176

Gnomad4 SAS exome

AF:

0.226

Gnomad4 FIN exome

AF:

0.191

Gnomad4 NFE exome

AF:

0.204

Gnomad4 OTH exome

AF:

0.206

GnomAD4 genome

AF:

0.168

AC:

25629

AN:

152236

Hom.:

2385

Cov.:

AF XY:

0.169

AC XY:

12564

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.0866

Gnomad4 AMR

AF:

0.155

Gnomad4 ASJ

AF:

0.246

Gnomad4 EAS

AF:

0.180

Gnomad4 SAS

AF:

0.215

Gnomad4 FIN

AF:

0.190

Gnomad4 NFE

AF:

0.207

Gnomad4 OTH

AF:

0.211

Alfa

AF:

0.199

Hom.:

2875

Bravo

AF:

0.162

Asia WGS

AF:

0.171

AC:

599

AN:

3478

EpiCase

AF:

0.236

EpiControl

AF:

0.232

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Genetic Services Laboratory, University of Chicago

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Jan 14, 2016

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Microcephalic primordial dwarfism due to RTTN deficiency

Benign:1

May 18, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

3.4

DANN

Benign

0.77

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