rs841224

chr16-4686833-G-Achr16-4686833-G-Cchr16-4686833-G-T

Variant summary

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

The ENST00000399577.9(MGRN1):c.*534G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 985,992 control chromosomes in the GnomAD database, including 165,326 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 0.53 (21923 hom., cov: 33)
  • Exomes 𝑓: 0.59 (143403 hom.)
• Consequence: MGRN1 ENST00000399577.9 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526

Genes affected

MGRN1 (HGNC:20254): (mahogunin ring finger 1) Enables ubiquitin-protein transferase activity. Involved in endosome to lysosome transport; negative regulation of signal transduction; and protein monoubiquitination. Located in several cellular components, including early endosome; endoplasmic reticulum; and nucleus. [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 (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGRN1	NM_015246.4	c.1619-1963G>A		intron_variant		ENST00000262370.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGRN1	ENST00000262370.12	c.1619-1963G>A		intron_variant		1	NM_015246.4	A1

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80502 AN: 151946 Hom.: 21885 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.511

GnomAD4 exome AF: 0.585 AC: 487850 AN: 833928 Hom.: 143403 Cov.: 33 AF XY: 0.585 AC XY: 225331 AN XY: 385148

Gnomad4 AFR exome AF: 0.436

Gnomad4 AMR exome AF: 0.485

Gnomad4 ASJ exome AF: 0.524

Gnomad4 EAS exome AF: 0.629

Gnomad4 SAS exome AF: 0.435

Gnomad4 FIN exome AF: 0.563

Gnomad4 NFE exome AF: 0.592

Gnomad4 OTH exome AF: 0.567

GnomAD4 genome AF: 0.530 AC: 80586 AN: 152064 Hom.: 21923 Cov.: 33 AF XY: 0.527 AC XY: 39174 AN XY: 74346

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.505

Alfa AF: 0.482 Hom.: 2612

Bravo AF: 0.522

Asia WGS AF: 0.505 AC: 1757 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	0.45
Dann	Benign	0.85

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: rs841224; hg19: chr16-4736834;