rs3743761

chr16-77193987-C-G

Variant summary

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

The NM_014940.4(MON1B):c.475+210C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 611,402 control chromosomes in the GnomAD database, including 136,186 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 0.69 (37739 hom., cov: 31)
  • Exomes 𝑓: 0.65 (98447 hom.)
• Consequence: MON1B NM_014940.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71

Genes affected

MON1B (HGNC:25020): (MON1 homolog B, secretory trafficking associated) Involved in early viral transcription and late viral transcription. Located in cytoplasm. Part of Mon1-Ccz1 complex. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MON1B	NM_014940.4	c.475+210C>G		intron_variant		ENST00000248248.8
MON1B	NM_001286639.2	c.149-348C>G		intron_variant
MON1B	NM_001286640.2	c.38-348C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MON1B	ENST00000248248.8	c.475+210C>G		intron_variant		1	NM_014940.4	P1

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105418 AN: 151758 Hom.: 37694 Cov.: 31

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.691

GnomAD4 exome AF: 0.648 AC: 297887 AN: 459526 Hom.: 98447 Cov.: 5 AF XY: 0.652 AC XY: 157055 AN XY: 241032

Gnomad4 AFR exome AF: 0.858

Gnomad4 AMR exome AF: 0.747

Gnomad4 ASJ exome AF: 0.621

Gnomad4 EAS exome AF: 0.850

Gnomad4 SAS exome AF: 0.728

Gnomad4 FIN exome AF: 0.561

Gnomad4 NFE exome AF: 0.607

Gnomad4 OTH exome AF: 0.654

GnomAD4 genome AF: 0.695 AC: 105522 AN: 151876 Hom.: 37739 Cov.: 31 AF XY: 0.695 AC XY: 51552 AN XY: 74192

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.853

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.695

Alfa AF: 0.658 Hom.: 4199

Bravo AF: 0.712

Asia WGS AF: 0.826 AC: 2869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.0030
Dann	Benign	0.64
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs3743761; hg19: chr16-77227884;