rs2766545

Variant names:

• chr6-35745254-A-C
• rs2766545
• NM_001286574.2:c.445-2007A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-35745254-A-C
• chr6-35745254-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001286574.2(ARMC12):​c.445-2007A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ARMC12 NM_001286574.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 2 publications found

Genes affected

ARMC12 (HGNC:21099): (armadillo repeat containing 12) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286574.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMC12	NM_001286574.2	MANE Select	c.445-2007A>C		intron	N/A	NP_001273503.1	Q5T9G4-1
	ARMC12	NM_145028.5		c.526-2007A>C		intron	N/A	NP_659465.2
	ARMC12	NM_001286576.2		c.445-2007A>C		intron	N/A	NP_001273505.1	Q5T9G4-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMC12	ENST00000373866.4	TSL:3 MANE Select	c.445-2007A>C		intron	N/A	ENSP00000362973.3	Q5T9G4-1
	ARMC12	ENST00000288065.6	TSL:1	c.526-2007A>C		intron	N/A	ENSP00000288065.2	Q5T9G4-2
	ARMC12	ENST00000373869.7	TSL:2	c.445-2007A>C		intron	N/A	ENSP00000362976.3	Q5T9G4-3

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		-0.039

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

Other links and lift over

dbSNP: rs2766545; hg19: chr6-35713031;