rs2288440

chr5-16710463-A-Gchr5-16710463-A-T

Variant summary

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

The NM_012334.3(MYO10):c.2169+445T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,010 control chromosomes in the GnomAD database, including 9,729 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 0.35 (9729 hom., cov: 32)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.26

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO10	NM_012334.3	c.2169+445T>C		intron_variant		ENST00000513610.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO10	ENST00000513610.6	c.2169+445T>C		intron_variant		1	NM_012334.3	P1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52784 AN: 151892 Hom.: 9723 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.348 AC: 52842 AN: 152010 Hom.: 9729 Cov.: 32 AF XY: 0.349 AC XY: 25939 AN XY: 74306

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.323

Alfa AF: 0.308 Hom.: 3497

Bravo AF: 0.352

Asia WGS AF: 0.372 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.023
Dann	Benign	0.21

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2288440; hg19: chr5-16710572;