chr16-77193987-C-G

Variant names:

• chr16-77193987-C-G
• rs3743761
• NM_014940.4:c.475+210C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MON1B	NM_014940.4	c.475+210C>G		intron_variant	Intron 3 of 5	ENST00000248248.8	NP_055755.1
MON1B	NM_001286639.2	c.149-348C>G		intron_variant	Intron 2 of 4		NP_001273568.1
MON1B	NM_001286640.2	c.38-348C>G		intron_variant	Intron 1 of 3		NP_001273569.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MON1B	ENST00000248248.8	c.475+210C>G		intron_variant	Intron 3 of 5	1	NM_014940.4	ENSP00000248248.3

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

African (AFR) AF: 0.858 AC: 10856 AN: 12652

American (AMR) AF: 0.747 AC: 13577 AN: 18166

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 8540 AN: 13746

East Asian (EAS) AF: 0.850 AC: 26422 AN: 31078

South Asian (SAS) AF: 0.728 AC: 33107 AN: 45478

European-Finnish (FIN) AF: 0.561 AC: 16804 AN: 29944

Middle Eastern (MID) AF: 0.732 AC: 1463 AN: 1998

European-Non Finnish (NFE) AF: 0.607 AC: 169954 AN: 280208

Other (OTH) AF: 0.654 AC: 17164 AN: 26256

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

African (AFR) AF: 0.855 AC: 35391 AN: 41406

American (AMR) AF: 0.728 AC: 11123 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2128 AN: 3464

East Asian (EAS) AF: 0.853 AC: 4368 AN: 5118

South Asian (SAS) AF: 0.716 AC: 3451 AN: 4820

European-Finnish (FIN) AF: 0.544 AC: 5741 AN: 10546

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41097 AN: 67928

Other (OTH) AF: 0.695 AC: 1465 AN: 2108

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
PhyloP100		-2.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs3743761; hg19: chr16-77227884;