Genetic Variant MYO5B:c.2004-15_2004-13dupTTT (chr18-49929610-G-GAAA) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_001080467.3(MYO5B):c.2004-15_2004-13dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000023 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00041 ( 0 hom. )

Consequence

MYO5B
NM_001080467.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.06

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:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS1

Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.000415 (479/1155242) while in subpopulation SAS AF= 0.000569 (40/70330). AF 95% confidence interval is 0.000429. There are 0 homozygotes in gnomad4_exome. There are 246 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO5B	NM_001080467.3 link	c.2004-15_2004-13dupTTT		intron_variant	Intron 16 of 39	ENST00000285039.12	NP_001073936.1	Q9ULV0-1Q7Z7A5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO5B	ENST00000285039.12 link	c.2004-13_2004-12insTTT		intron_variant	Intron 16 of 39	1	NM_001080467.3	ENSP00000285039.6		Q9ULV0-1
MYO5B	ENST00000697219.1 link	c.1800-13_1800-12insTTT		intron_variant	Intron 14 of 37			ENSP00000513188.1		A0A8V8TM52

Frequencies

GnomAD3 genomes

AF:

0.0000301

AC:

AN:

132862

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00352

Gnomad NFE

AF:

0.0000480

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000415

AC:

479

AN:

1155242

Hom.:

Cov.:

AF XY:

0.000426

AC XY:

246

AN XY:

577444

show subpopulations

Gnomad4 AFR exome

AF:

0.0000376

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.000450

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000569

Gnomad4 FIN exome

AF:

0.000193

Gnomad4 NFE exome

AF:

0.000462

Gnomad4 OTH exome

AF:

0.000265

GnomAD4 genome

AF:

0.0000226

AC:

AN:

132840

Hom.:

Cov.:

AF XY:

0.0000315

AC XY:

AN XY:

63450

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000480

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

18-49929610-GAAAAAAA-GAAAAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over