rs2817041

chr6-35738115-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001286574.2(ARMC12):c.252T>C(p.Tyr84=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 1,613,732 control chromosomes in the GnomAD database, including 513,953 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 0.79 (48053 hom., cov: 31)
  • Exomes 𝑓: 0.80 (465900 hom.)
• Consequence: ARMC12 NM_001286574.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP7: Synonymous conserved (PhyloP=0.487 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARMC12	NM_001286574.2	c.252T>C	p.Tyr84=	synonymous_variant	2/6	ENST00000373866.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMC12	ENST00000373866.4	c.252T>C	p.Tyr84=	synonymous_variant	2/6	3	NM_001286574.2	A1
ARMC12	ENST00000288065.6	c.333T>C	p.Tyr111=	synonymous_variant	2/6	1		P3
ARMC12	ENST00000373869.7	c.252T>C	p.Tyr84=	synonymous_variant	2/6	2
ARMC12	ENST00000471400.1	c.*112T>C		3_prime_UTR_variant, NMD_transcript_variant	2/3	3

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120557 AN: 151912 Hom.: 47999 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.809

GnomAD3 exomes AF: 0.794 AC: 199495 AN: 251280 Hom.: 79751 AF XY: 0.790 AC XY: 107315 AN XY: 135824

Gnomad AFR exome AF: 0.787

Gnomad AMR exome AF: 0.847

Gnomad ASJ exome AF: 0.796

Gnomad EAS exome AF: 0.599

Gnomad SAS exome AF: 0.758

Gnomad FIN exome AF: 0.842

Gnomad NFE exome AF: 0.810

Gnomad OTH exome AF: 0.800

GnomAD4 exome AF: 0.797 AC: 1165229 AN: 1461702 Hom.: 465900 Cov.: 72 AF XY: 0.796 AC XY: 578832 AN XY: 727160

Gnomad4 AFR exome AF: 0.786

Gnomad4 AMR exome AF: 0.845

Gnomad4 ASJ exome AF: 0.802

Gnomad4 EAS exome AF: 0.600

Gnomad4 SAS exome AF: 0.758

Gnomad4 FIN exome AF: 0.838

Gnomad4 NFE exome AF: 0.804

Gnomad4 OTH exome AF: 0.796

GnomAD4 genome AF: 0.794 AC: 120671 AN: 152030 Hom.: 48053 Cov.: 31 AF XY: 0.792 AC XY: 58811 AN XY: 74298

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.812

Alfa AF: 0.799 Hom.: 22030

Bravo AF: 0.796

Asia WGS AF: 0.754 AC: 2622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	6.9
Dann	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2817041; hg19: chr6-35705892; COSMIC: COSV55361145; COSMIC: COSV55361145;