18-49877754-A-G

Position:

• chr18-49877754-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001080467.3(MYO5B):​c.3396+9T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0549 in 1,613,816 control chromosomes in the GnomAD database, including 3,302 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.042 (177 hom., cov: 32)
  • Exomes 𝑓: 0.056 (3125 hom.)
• Consequence: MYO5B NM_001080467.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: 0.0720

Genes affected

MYO5B (HGNC:7603): (myosin VB) The protein encoded by this gene, together with other proteins, may be involved in plasma membrane recycling. Mutations in this gene are associated with microvillous inclusion disease. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 18-49877754-A-G is Benign according to our data. Variant chr18-49877754-A-G is described in ClinVar as [Benign]. Clinvar id is 327028.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO5B	NM_001080467.3	c.3396+9T>C		intron_variant		ENST00000285039.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO5B	ENST00000285039.12	c.3396+9T>C		intron_variant		1	NM_001080467.3	P1

Frequencies

GnomAD3 genomes AF: 0.0422 AC: 6423 AN: 152170 Hom.: 177 Cov.: 32

Gnomad AFR AF: 0.0217

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.00655

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0602

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0494

Gnomad OTH AF: 0.0406

GnomAD3 exomes AF: 0.0576 AC: 14368 AN: 249398 Hom.: 743 AF XY: 0.0644 AC XY: 8710 AN XY: 135300

Gnomad AFR exome AF: 0.0201

Gnomad AMR exome AF: 0.0221

Gnomad ASJ exome AF: 0.0698

Gnomad EAS exome AF: 0.00506

Gnomad SAS exome AF: 0.168

Gnomad FIN exome AF: 0.0606

Gnomad NFE exome AF: 0.0504

Gnomad OTH exome AF: 0.0578

GnomAD4 exome AF: 0.0562 AC: 82162 AN: 1461528 Hom.: 3125 Cov.: 32 AF XY: 0.0600 AC XY: 43630 AN XY: 727072

Gnomad4 AFR exome AF: 0.0219

Gnomad4 AMR exome AF: 0.0229

Gnomad4 ASJ exome AF: 0.0697

Gnomad4 EAS exome AF: 0.00348

Gnomad4 SAS exome AF: 0.164

Gnomad4 FIN exome AF: 0.0617

Gnomad4 NFE exome AF: 0.0514

Gnomad4 OTH exome AF: 0.0566

GnomAD4 genome AF: 0.0422 AC: 6428 AN: 152288 Hom.: 177 Cov.: 32 AF XY: 0.0447 AC XY: 3328 AN XY: 74450

Gnomad4 AFR AF: 0.0218

Gnomad4 AMR AF: 0.0271

Gnomad4 ASJ AF: 0.0617

Gnomad4 EAS AF: 0.00656

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.0602

Gnomad4 NFE AF: 0.0494

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0487 Hom.: 97

Bravo AF: 0.0370

Asia WGS AF: 0.0870 AC: 304 AN: 3478

EpiCase AF: 0.0527

EpiControl AF: 0.0511

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Congenital microvillous atrophy Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Sep 05, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 30, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 10, 2019	This variant is associated with the following publications: (PMID: 29266534) -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.3
DANN	Benign	0.38
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: rs75971548; hg19: chr18-47404124;