6-35737829-G-A

Position:

• chr6-35737829-G-A

Variant summary

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

The NM_001286574.2(ARMC12):​c.164-198G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,142 control chromosomes in the GnomAD database, including 4,290 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 0.23 (4290 hom., cov: 32)
• Consequence: ARMC12 NM_001286574.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.853

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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARMC12	NM_001286574.2	c.164-198G>A		intron_variant		ENST00000373866.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMC12	ENST00000373866.4	c.164-198G>A		intron_variant		3	NM_001286574.2	A1
ARMC12	ENST00000288065.6	c.245-198G>A		intron_variant		1		P3
ARMC12	ENST00000373869.7	c.164-198G>A		intron_variant		2
ARMC12	ENST00000471400.1	c.164-170G>A		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34418 AN: 152024 Hom.: 4286 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.226 AC: 34425 AN: 152142 Hom.: 4290 Cov.: 32 AF XY: 0.229 AC XY: 17012 AN XY: 74378

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.249

Alfa AF: 0.262 Hom.: 10869

Bravo AF: 0.222

Asia WGS AF: 0.300 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.2
DANN	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2817040; hg19: chr6-35705606; COSMIC: COSV55362271; COSMIC: COSV55362271;