5-16922272-G-T

Variant names:

• chr5-16922272-G-T
• rs249120
• NM_012334.3:c.21+13516C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000513610.6(MYO10):​c.21+13516C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 151,560 control chromosomes in the GnomAD database, including 48,814 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 0.80 (48814 hom., cov: 29)
• Consequence: MYO10 ENST00000513610.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 1 publications found

Genes affected

MYO10 (HGNC:7593): (myosin X) This gene encodes a member of the myosin superfamily. The protein represents an unconventional myosin; it should not be confused with the conventional non-muscle myosin-10 (MYH10). Unconventional myosins contain the basic domains of conventional myosins and are further distinguished from class members by their tail domains. This gene functions as an actin-based molecular motor and plays a role in integration of F-actin and microtubule cytoskeletons during meiosis. [provided by RefSeq, Dec 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513610.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO10	NM_012334.3	MANE Select	c.21+13516C>A		intron	N/A	NP_036466.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO10	ENST00000513610.6	TSL:1 MANE Select	c.21+13516C>A		intron	N/A	ENSP00000421280.1
	MYO10	ENST00000507288.1	TSL:1	c.21+13516C>A		intron	N/A	ENSP00000426664.1
	MYO10	ENST00000274203.13	TSL:5	c.21+13516C>A		intron	N/A	ENSP00000274203.10

Frequencies

GnomAD3 genomes AF: 0.798 AC: 120864 AN: 151446 Hom.: 48777 Cov.: 29

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.835

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.798 AC: 120953 AN: 151560 Hom.: 48814 Cov.: 29 AF XY: 0.797 AC XY: 58962 AN XY: 73978

African (AFR) AF: 0.915 AC: 37850 AN: 41360

American (AMR) AF: 0.772 AC: 11743 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2498 AN: 3470

East Asian (EAS) AF: 0.881 AC: 4509 AN: 5116

South Asian (SAS) AF: 0.816 AC: 3919 AN: 4800

European-Finnish (FIN) AF: 0.724 AC: 7536 AN: 10402

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50304 AN: 67908

Other (OTH) AF: 0.780 AC: 1636 AN: 2098

Alfa AF: 0.757 Hom.: 21825

Bravo AF: 0.807

Asia WGS AF: 0.834 AC: 2901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.64
PhyloP100		-0.54
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: rs249120; hg19: chr5-16922381;