Variant 18-49823176-A-AT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001080467.3(MYO5B):c.*3294_*3295insA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.38 ( 0 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

MYO5B
NM_001080467.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.122

Variant links:

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]

MYO5B links:

SNHG22 (HGNC:50285): (small nucleolar RNA host gene 22)

SNHG22 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO5B	NM_001080467.3 linkuse as main transcript	c.3294_3295insA		3_prime_UTR_variant	40/40	ENST00000285039.12
SNHG22	NR_117096.1 linkuse as main transcript	n.40+9114_40+9115insT		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO5B	ENST00000285039.12 linkuse as main transcript	c.3294_3295insA		3_prime_UTR_variant	40/40	1	NM_001080467.3	P1	Q9ULV0-1
SNHG22	ENST00000589499.1 linkuse as main transcript	n.40+9114_40+9115insT		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

21769

AN:

57316

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.374

Gnomad AMI

AF:

0.382

Gnomad AMR

AF:

0.379

Gnomad ASJ

AF:

0.378

Gnomad EAS

AF:

0.394

Gnomad SAS

AF:

0.353

Gnomad FIN

AF:

0.375

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.385

Gnomad OTH

AF:

0.358

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.380

AC:

21796

AN:

57378

Hom.:

Cov.:

AF XY:

0.371

AC XY:

10512

AN XY:

28316

show subpopulations

Gnomad4 AFR

AF:

0.375

Gnomad4 AMR

AF:

0.379

Gnomad4 ASJ

AF:

0.378

Gnomad4 EAS

AF:

0.393

Gnomad4 SAS

AF:

0.353

Gnomad4 FIN

AF:

0.375

Gnomad4 NFE

AF:

0.385

Gnomad4 OTH

AF:

0.359

Alfa

AF:

0.431

Hom.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Diarrhea with Microvillus Atrophy

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over