rs515324

Positions:

• chr18-49832262-G-A
• chr18-49832262-G-C
• chr18-49832262-G-T

Variant summary

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

The NM_001080467.3(MYO5B):​c.5394+3082C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 152,126 control chromosomes in the GnomAD database, including 42,933 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 0.75 (42933 hom., cov: 32)
• Consequence: MYO5B NM_001080467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO5B	NM_001080467.3	c.5394+3082C>T		intron_variant		ENST00000285039.12	NP_001073936.1
SNHG22	NR_117096.1	n.41-7014G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO5B	ENST00000285039.12	c.5394+3082C>T		intron_variant		1	NM_001080467.3	ENSP00000285039	P1
SNHG22	ENST00000589499.1	n.41-7014G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.750 AC: 114076 AN: 152008 Hom.: 42897 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.750 AC: 114167 AN: 152126 Hom.: 42933 Cov.: 32 AF XY: 0.753 AC XY: 55996 AN XY: 74368

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.786

Alfa AF: 0.745 Hom.: 18513

Bravo AF: 0.762

Asia WGS AF: 0.816 AC: 2835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.58
DANN	Benign	0.18

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: rs515324; hg19: chr18-47358632;