rs2766542

Positions:

• chr6-35739913-A-G

Variant summary

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

The NM_001286574.2(ARMC12):​c.444+1395A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,062 control chromosomes in the GnomAD database, including 31,756 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 0.64 (31756 hom., cov: 31)
• Consequence: ARMC12 NM_001286574.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

Genes affected

ARMC12 (HGNC:21099): (armadillo repeat containing 12) Located in nucleus. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARMC12	NM_001286574.2	c.444+1395A>G		intron_variant		ENST00000373866.4	NP_001273503.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARMC12	ENST00000373866.4	c.444+1395A>G		intron_variant		3	NM_001286574.2	ENSP00000362973.3
ARMC12	ENST00000288065.6	c.525+1395A>G		intron_variant		1		ENSP00000288065.2
ARMC12	ENST00000373869.7	c.444+1395A>G		intron_variant		2		ENSP00000362976.3

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96674 AN: 151942 Hom.: 31703 Cov.: 31

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.636 AC: 96780 AN: 152062 Hom.: 31756 Cov.: 31 AF XY: 0.635 AC XY: 47212 AN XY: 74318

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.622

Alfa AF: 0.595 Hom.: 6262

Bravo AF: 0.637

Asia WGS AF: 0.603 AC: 2098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.70
DANN	Benign	0.55

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: rs2766542; hg19: chr6-35707690;