rs17707882

Variant names:

• chr5-16864523-C-T
• rs17707882
• NM_012334.3:c.120+13086G>A

Variant summary

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

The NM_012334.3(MYO10):​c.120+13086G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0497 in 152,186 control chromosomes in the GnomAD database, including 274 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 0.050 (274 hom., cov: 32)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.89
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012334.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO10	NM_012334.3	MANE Select	c.120+13086G>A		intron	N/A	NP_036466.2	Q9HD67-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO10	ENST00000513610.6	TSL:1 MANE Select	c.120+13086G>A		intron	N/A	ENSP00000421280.1	Q9HD67-1
	MYO10	ENST00000507288.1	TSL:1	c.120+13086G>A		intron	N/A	ENSP00000426664.1	Q9HD67-2
	MYO10	ENST00000274203.13	TSL:5	c.120+13086G>A		intron	N/A	ENSP00000274203.10	A0A0A0MQX1

Frequencies

GnomAD3 genomes AF: 0.0497 AC: 7558 AN: 152068 Hom.: 275 Cov.: 32

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0470

Gnomad OTH AF: 0.0523

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

GnomAD4 genome AF: 0.0497 AC: 7563 AN: 152186 Hom.: 274 Cov.: 32 AF XY: 0.0519 AC XY: 3864 AN XY: 74408

African (AFR) AF: 0.0391 AC: 1625 AN: 41544

American (AMR) AF: 0.0320 AC: 489 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3470

East Asian (EAS) AF: 0.119 AC: 614 AN: 5146

South Asian (SAS) AF: 0.165 AC: 798 AN: 4826

European-Finnish (FIN) AF: 0.0560 AC: 594 AN: 10604

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0470 AC: 3197 AN: 67996

Other (OTH) AF: 0.0550 AC: 116 AN: 2108

Alfa AF: 0.0473 Hom.: 412

Bravo AF: 0.0454

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.54
PhyloP100		-3.9
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: rs17707882; hg19: chr5-16864632;