Variant 2-231208199-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001352754.2(ARMC9):c.124T>C(p.Leu42=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 1,607,608 control chromosomes in the GnomAD database, including 52,228 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6433 hom., cov: 33)

Exomes 𝑓: 0.25 ( 45795 hom. )

Consequence

ARMC9
NM_001352754.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.0180

Variant links:

Genes affected

ARMC9 (HGNC:20730): (armadillo repeat containing 9) Predicted to be involved in cilium assembly and positive regulation of smoothened signaling pathway. Located in centriole and ciliary basal body. Implicated in Joubert syndrome 30. [provided by Alliance of Genome Resources, Apr 2022]

ARMC9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 2-231208199-T-C is Benign according to our data. Variant chr2-231208199-T-C is described in ClinVar as [Benign]. Clinvar id is 1167998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.018 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARMC9	NM_001352754.2 linkuse as main transcript	c.124T>C	p.Leu42=	synonymous_variant	3/25	ENST00000611582.5	NP_001339683.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARMC9	ENST00000611582.5 linkuse as main transcript	c.124T>C	p.Leu42=	synonymous_variant	3/25	5	NM_001352754.2	ENSP00000484804	P1	Q7Z3E5-1

Frequencies

GnomAD3 genomes

AF:

0.284

AC:

43202

AN:

152006

Hom.:

6427

Cov.:

show subpopulations

Gnomad AFR

AF:

0.360

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.243

Gnomad ASJ

AF:

0.337

Gnomad EAS

AF:

0.146

Gnomad SAS

AF:

0.178

Gnomad FIN

AF:

0.359

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.292

GnomAD3 exomes

AF:

0.255

AC:

63014

AN:

247226

Hom.:

8652

AF XY:

0.251

AC XY:

33592

AN XY:

133648

show subpopulations

Gnomad AFR exome

AF:

0.364

Gnomad AMR exome

AF:

0.246

Gnomad ASJ exome

AF:

0.318

Gnomad EAS exome

AF:

0.146

Gnomad SAS exome

AF:

0.178

Gnomad FIN exome

AF:

0.352

Gnomad NFE exome

AF:

0.255

Gnomad OTH exome

AF:

0.269

GnomAD4 exome

AF:

0.247

AC:

359555

AN:

1455484

Hom.:

45795

Cov.:

AF XY:

0.245

AC XY:

177278

AN XY:

724002

show subpopulations

Gnomad4 AFR exome

AF:

0.364

Gnomad4 AMR exome

AF:

0.249

Gnomad4 ASJ exome

AF:

0.323

Gnomad4 EAS exome

AF:

0.176

Gnomad4 SAS exome

AF:

0.180

Gnomad4 FIN exome

AF:

0.350

Gnomad4 NFE exome

AF:

0.244

Gnomad4 OTH exome

AF:

0.245

GnomAD4 genome

AF:

0.284

AC:

43242

AN:

152124

Hom.:

6433

Cov.:

AF XY:

0.284

AC XY:

21148

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.360

Gnomad4 AMR

AF:

0.243

Gnomad4 ASJ

AF:

0.337

Gnomad4 EAS

AF:

0.147

Gnomad4 SAS

AF:

0.177

Gnomad4 FIN

AF:

0.359

Gnomad4 NFE

AF:

0.253

Gnomad4 OTH

AF:

0.289

Alfa

AF:

0.273

Hom.:

2977

Bravo

AF:

0.282

Asia WGS

AF:

0.194

AC:

676

AN:

3478

EpiCase

AF:

0.254

EpiControl

AF:

0.257

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 11, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.4

DANN

Benign

0.71

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