5-16885748-T-C

Variant names:

• chr5-16885748-T-C
• rs2562339
• NM_012334.3:c.22-8041A>G

Variant summary

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

The NM_012334.3(MYO10):​c.22-8041A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 151,778 control chromosomes in the GnomAD database, including 29,100 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 0.61 (29100 hom., cov: 31)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.06
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 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.22-8041A>G		intron	N/A	NP_036466.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO10	ENST00000513610.6	TSL:1 MANE Select	c.22-8041A>G		intron	N/A	ENSP00000421280.1
	MYO10	ENST00000507288.1	TSL:1	c.22-8041A>G		intron	N/A	ENSP00000426664.1
	MYO10	ENST00000274203.13	TSL:5	c.22-8041A>G		intron	N/A	ENSP00000274203.10

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92381 AN: 151668 Hom.: 29043 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.609 AC: 92493 AN: 151778 Hom.: 29100 Cov.: 31 AF XY: 0.604 AC XY: 44822 AN XY: 74162

African (AFR) AF: 0.775 AC: 32093 AN: 41414

American (AMR) AF: 0.616 AC: 9410 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2018 AN: 3472

East Asian (EAS) AF: 0.559 AC: 2871 AN: 5134

South Asian (SAS) AF: 0.454 AC: 2182 AN: 4802

European-Finnish (FIN) AF: 0.517 AC: 5422 AN: 10490

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.537 AC: 36488 AN: 67892

Other (OTH) AF: 0.579 AC: 1220 AN: 2106

Alfa AF: 0.530 Hom.: 11380

Bravo AF: 0.629

Asia WGS AF: 0.530 AC: 1844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.067
DANN	Benign	0.34
PhyloP100		-3.1
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: rs2562339; hg19: chr5-16885857;