6-151468220-T-G

Variant names:

• chr6-151468220-T-G
• rs963193
• NM_024573.3:c.559-123T>G

Variant summary

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

The NM_024573.3(ARMT1):​c.559-123T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 620,922 control chromosomes in the GnomAD database, including 75,907 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 0.54 (25057 hom., cov: 33)
  • Exomes 𝑓: 0.45 (50850 hom.)
• Consequence: ARMT1 NM_024573.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

Genes affected

ARMT1 (HGNC:17872): (acidic residue methyltransferase 1) Enables S-adenosylmethionine-dependent methyltransferase activity; enzyme binding activity; and protein carboxyl O-methyltransferase activity. Involved in methylation and regulation of response to DNA damage stimulus. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARMT1	NM_024573.3	c.559-123T>G		intron_variant	Intron 4 of 4	ENST00000367294.4	NP_078849.1
ARMT1	NM_001286562.2	c.202-123T>G		intron_variant	Intron 3 of 3		NP_001273491.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARMT1	ENST00000367294.4	c.559-123T>G		intron_variant	Intron 4 of 4	1	NM_024573.3	ENSP00000356263.3
ARMT1	ENST00000545879.5	c.202-123T>G		intron_variant	Intron 3 of 3	2		ENSP00000444121.1
ARMT1	ENST00000494826.1	n.*282-123T>G		intron_variant	Intron 3 of 3	2		ENSP00000435882.1

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82360 AN: 151990 Hom.: 25003 Cov.: 33

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.529

GnomAD4 exome AF: 0.451 AC: 211475 AN: 468814 Hom.: 50850 AF XY: 0.452 AC XY: 111735 AN XY: 246962

Gnomad4 AFR exome AF: 0.820

Gnomad4 AMR exome AF: 0.450

Gnomad4 ASJ exome AF: 0.452

Gnomad4 EAS exome AF: 0.704

Gnomad4 SAS exome AF: 0.530

Gnomad4 FIN exome AF: 0.392

Gnomad4 NFE exome AF: 0.401

Gnomad4 OTH exome AF: 0.474

GnomAD4 genome AF: 0.542 AC: 82467 AN: 152108 Hom.: 25057 Cov.: 33 AF XY: 0.544 AC XY: 40450 AN XY: 74354

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.534

Alfa AF: 0.445 Hom.: 7681

Bravo AF: 0.560

Asia WGS AF: 0.657 AC: 2273 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.66

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: rs963193; hg19: chr6-151789355; COSMIC: COSV66178364; COSMIC: COSV66178364;