rs7301016

chr12-62492343-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MON2	NM_015026.3	c.176-1572A>G		intron_variant		ENST00000393630.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MON2	ENST00000393630.8	c.176-1572A>G		intron_variant		1	NM_015026.3	P4

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

Gnomad4 AFR AF: 0.0352

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0192

Gnomad4 SAS AF: 0.0812

Gnomad4 FIN AF: 0.0842

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.142

Alfa AF: 0.132 Hom.: 190

Bravo AF: 0.115

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	10
Dann	Benign	0.86

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: rs7301016; hg19: chr12-62886123;