chr5-16864523-C-T

Position:

• chr5-16864523-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO10	NM_012334.3	c.120+13086G>A		intron_variant		ENST00000513610.6
MYO10	XM_006714475.4	c.120+13086G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO10	ENST00000513610.6	c.120+13086G>A		intron_variant		1	NM_012334.3	P1

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

Gnomad4 AFR AF: 0.0391

Gnomad4 AMR AF: 0.0320

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0560

Gnomad4 NFE AF: 0.0470

Gnomad4 OTH AF: 0.0550

Alfa AF: 0.0483 Hom.: 313

Bravo AF: 0.0454

Asia WGS AF: 0.148 AC: 514 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	0.15
DANN	Benign	0.54

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: rs17707882; hg19: chr5-16864632;