5-16690645-C-T

Variant names:

• chr5-16690645-C-T
• rs31313
• NM_012334.3:c.3801-726G>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.3801-726G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 151,956 control chromosomes in the GnomAD database, including 2,558 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 0.17 (2558 hom., cov: 31)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.59
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.252 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.3801-726G>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.3801-726G>A		intron	N/A	ENSP00000421280.1	Q9HD67-1
	MYO10	ENST00000274203.13	TSL:5	c.3834-726G>A		intron	N/A	ENSP00000274203.10	A0A0A0MQX1
	MYO10	ENST00000505695.5	TSL:2	c.1818-726G>A		intron	N/A	ENSP00000421170.1	E9PEW5

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26180 AN: 151836 Hom.: 2558 Cov.: 31

Gnomad AFR AF: 0.0856

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.172 AC: 26185 AN: 151956 Hom.: 2558 Cov.: 31 AF XY: 0.179 AC XY: 13255 AN XY: 74236

African (AFR) AF: 0.0856 AC: 3551 AN: 41504

American (AMR) AF: 0.251 AC: 3833 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 653 AN: 3470

East Asian (EAS) AF: 0.264 AC: 1343 AN: 5094

South Asian (SAS) AF: 0.166 AC: 798 AN: 4812

European-Finnish (FIN) AF: 0.257 AC: 2707 AN: 10530

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.187 AC: 12721 AN: 67982

Other (OTH) AF: 0.196 AC: 413 AN: 2104

Alfa AF: 0.183 Hom.: 11854

Bravo AF: 0.168

Asia WGS AF: 0.207 AC: 718 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.77
DANN	Benign	0.55
PhyloP100		-3.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs31313; hg19: chr5-16690754;