rs2766543

Positions:

• chr6-35740857-G-T

Variant summary

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

The NM_001286574.2(ARMC12):​c.444+2339G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 150,708 control chromosomes in the GnomAD database, including 27,004 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 0.58 (27004 hom., cov: 28)
• Consequence: ARMC12 NM_001286574.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARMC12	NM_001286574.2	c.444+2339G>T		intron_variant		ENST00000373866.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMC12	ENST00000373866.4	c.444+2339G>T		intron_variant		3	NM_001286574.2	A1
ARMC12	ENST00000288065.6	c.525+2339G>T		intron_variant		1		P3
ARMC12	ENST00000373869.7	c.444+2339G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.583 AC: 87848 AN: 150590 Hom.: 26943 Cov.: 28

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.584 AC: 87968 AN: 150708 Hom.: 27004 Cov.: 28 AF XY: 0.582 AC XY: 42739 AN XY: 73444

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.556

Alfa AF: 0.511 Hom.: 33697

Bravo AF: 0.587

Asia WGS AF: 0.537 AC: 1869 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	0.13
DANN	Benign	0.36

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: rs2766543; hg19: chr6-35708634;