6-35745254-A-G

Position:

• chr6-35745254-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.445-2007A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,064 control chromosomes in the GnomAD database, including 27,810 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 0.59 (27810 hom., cov: 32)
• Consequence: ARMC12 NM_001286574.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARMC12	NM_001286574.2	c.445-2007A>G		intron_variant		ENST00000373866.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMC12	ENST00000373866.4	c.445-2007A>G		intron_variant		3	NM_001286574.2	A1
ARMC12	ENST00000288065.6	c.526-2007A>G		intron_variant		1		P3
ARMC12	ENST00000373869.7	c.445-2007A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89350 AN: 151946 Hom.: 27750 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.588 AC: 89469 AN: 152064 Hom.: 27810 Cov.: 32 AF XY: 0.586 AC XY: 43560 AN XY: 74330

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.562

Alfa AF: 0.513 Hom.: 26524

Bravo AF: 0.591

Asia WGS AF: 0.531 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.40

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: rs2766545; hg19: chr6-35713031;