rs515324

Variant names:

• chr18-49832262-G-A
• rs515324
• NM_001080467.3:c.5394+3082C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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]

ENSG00000266997 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MYO5B	NM_001080467.3	c.5394+3082C>T		intron_variant	Intron 39 of 39	ENST00000285039.12	NP_001073936.1
SNHG22	NR_117096.1	n.41-7014G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO5B	ENST00000285039.12	c.5394+3082C>T		intron_variant	Intron 39 of 39	1	NM_001080467.3	ENSP00000285039.6
ENSG00000266997	ENST00000590532.2	n.363+3082C>T		intron_variant	Intron 3 of 6	5		ENSP00000467396.2

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

African (AFR) AF: 0.717 AC: 29742 AN: 41478

American (AMR) AF: 0.846 AC: 12941 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2831 AN: 3470

East Asian (EAS) AF: 0.829 AC: 4285 AN: 5168

South Asian (SAS) AF: 0.764 AC: 3685 AN: 4824

European-Finnish (FIN) AF: 0.701 AC: 7409 AN: 10570

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50585 AN: 68000

Other (OTH) AF: 0.786 AC: 1659 AN: 2110

Alfa AF: 0.746 Hom.: 20933

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
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs515324; hg19: chr18-47358632;