rs506696

chr18-49836038-A-Cchr18-49836038-A-T

Variant summary

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

The NM_001080467.3(MYO5B):c.5314-614T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,000 control chromosomes in the GnomAD database, including 28,584 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 0.61 (28584 hom., cov: 32)
• Consequence: MYO5B NM_001080467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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]

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO5B	NM_001080467.3	c.5314-614T>G		intron_variant		ENST00000285039.12
SNHG22	NR_117096.1	n.41-3238A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO5B	ENST00000285039.12	c.5314-614T>G		intron_variant		1	NM_001080467.3	P1
SNHG22	ENST00000589499.1	n.41-3238A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92748 AN: 151882 Hom.: 28569 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.658

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.611 AC: 92809 AN: 152000 Hom.: 28584 Cov.: 32 AF XY: 0.607 AC XY: 45102 AN XY: 74276

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.655

Alfa AF: 0.602 Hom.: 53188

Bravo AF: 0.629

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.099
Dann	Benign	0.25

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: rs506696; hg19: chr18-47362408;