rs7301016

Variant names:

• chr12-62492343-A-G
• rs7301016
• NM_015026.3:c.176-1572A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015026.3(MON2):​c.176-1572A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 150,498 control chromosomes in the GnomAD database, including 1,245 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 0.11 (1245 hom., cov: 31)
• Consequence: MON2 NM_015026.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190
• Publications: 7 publications found

Genes affected

MON2 (HGNC:29177): (MON2 homolog, regulator of endosome-to-Golgi trafficking) Predicted to be involved in Golgi to endosome transport. Located in early endosome membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015026.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MON2	NM_015026.3	MANE Select	c.176-1572A>G		intron	N/A	NP_055841.2
	MON2	NM_001278470.2		c.176-1572A>G		intron	N/A	NP_001265399.1
	MON2	NM_001278471.2		c.176-1572A>G		intron	N/A	NP_001265400.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MON2	ENST00000393630.8	TSL:1 MANE Select	c.176-1572A>G		intron	N/A	ENSP00000377250.4
	MON2	ENST00000393629.6	TSL:1	c.176-1572A>G		intron	N/A	ENSP00000377249.2
	MON2	ENST00000552738.5	TSL:1	c.176-1572A>G		intron	N/A	ENSP00000449215.1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17007 AN: 150434 Hom.: 1244 Cov.: 31

Gnomad AFR AF: 0.0351

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.0814

Gnomad FIN AF: 0.0842

Gnomad MID AF: 0.235

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.113 AC: 17004 AN: 150498 Hom.: 1245 Cov.: 31 AF XY: 0.109 AC XY: 7983 AN XY: 73426

African (AFR) AF: 0.0352 AC: 1448 AN: 41150

American (AMR) AF: 0.129 AC: 1956 AN: 15134

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3462

East Asian (EAS) AF: 0.0192 AC: 98 AN: 5110

South Asian (SAS) AF: 0.0812 AC: 388 AN: 4776

European-Finnish (FIN) AF: 0.0842 AC: 833 AN: 9894

Middle Eastern (MID) AF: 0.243 AC: 69 AN: 284

European-Non Finnish (NFE) AF: 0.166 AC: 11256 AN: 67692

Other (OTH) AF: 0.142 AC: 296 AN: 2086

Alfa AF: 0.119 Hom.: 383

Bravo AF: 0.115

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	10
DANN	Benign	0.86
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7301016; hg19: chr12-62886123;