chr2-231322443-C-T

Position:

• chr2-231322443-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001352754.2(ARMC9):​c.1774-9350C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,184 control chromosomes in the GnomAD database, including 25,152 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (25152 hom., cov: 34)
• Consequence: ARMC9 NM_001352754.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.535

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARMC9	NM_001352754.2	c.1774-9350C>T		intron_variant		ENST00000611582.5	NP_001339683.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARMC9	ENST00000611582.5	c.1774-9350C>T		intron_variant		5	NM_001352754.2	ENSP00000484804	P1

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81456 AN: 152066 Hom.: 25100 Cov.: 34

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.536 AC: 81564 AN: 152184 Hom.: 25152 Cov.: 34 AF XY: 0.534 AC XY: 39713 AN XY: 74408

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.503

Alfa AF: 0.409 Hom.: 18447

Bravo AF: 0.547

Asia WGS AF: 0.571 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	14
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

Other links and lift over

dbSNP: rs6753112; hg19: chr2-232187155;