rs3757316

Positions:

• chr6-151453204-G-A

Variant summary

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

The NM_024573.3(ARMT1):​c.41+618G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,088 control chromosomes in the GnomAD database, including 17,265 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 0.46 (17265 hom., cov: 33)
• Consequence: ARMT1 NM_024573.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARMT1	NM_024573.3	c.41+618G>A		intron_variant		ENST00000367294.4
ARMT1	NM_001286562.2	c.-211+618G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMT1	ENST00000367294.4	c.41+618G>A		intron_variant		1	NM_024573.3	P1
ARMT1	ENST00000545879.5	c.-211+618G>A		intron_variant		2
ARMT1	ENST00000494826.1	c.41+618G>A		intron_variant, NMD_transcript_variant		2
ARMT1	ENST00000483931.1	n.277+404G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69200 AN: 151970 Hom.: 17239 Cov.: 33

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.455 AC: 69274 AN: 152088 Hom.: 17265 Cov.: 33 AF XY: 0.457 AC XY: 33953 AN XY: 74328

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.446

Alfa AF: 0.372 Hom.: 11753

Bravo AF: 0.473

Asia WGS AF: 0.540 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.6
DANN	Benign	0.57

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: rs3757316; hg19: chr6-151774339;