NM_012334.3:c.1930-14526T>C

Variant names:

• chr5-16725771-A-G
• rs173738
• NM_012334.3:c.1930-14526T>C

Variant summary

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

The NM_012334.3(MYO10):​c.1930-14526T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 150,502 control chromosomes in the GnomAD database, including 33,543 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 0.66 (33543 hom., cov: 28)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 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.1930-14526T>C		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.1930-14526T>C		intron	N/A	ENSP00000421280.1	Q9HD67-1
	MYO10	ENST00000274203.13	TSL:5	c.1930-14526T>C		intron	N/A	ENSP00000274203.10	A0A0A0MQX1
	MYO10	ENST00000505695.5	TSL:2	c.-54-14526T>C		intron	N/A	ENSP00000421170.1	E9PEW5

Frequencies

GnomAD3 genomes AF: 0.665 AC: 99991 AN: 150400 Hom.: 33508 Cov.: 28

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.665 AC: 100075 AN: 150502 Hom.: 33543 Cov.: 28 AF XY: 0.665 AC XY: 48771 AN XY: 73310

African (AFR) AF: 0.732 AC: 29939 AN: 40878

American (AMR) AF: 0.650 AC: 9839 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2151 AN: 3472

East Asian (EAS) AF: 0.577 AC: 2881 AN: 4992

South Asian (SAS) AF: 0.539 AC: 2562 AN: 4750

European-Finnish (FIN) AF: 0.696 AC: 7074 AN: 10160

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43599 AN: 67828

Other (OTH) AF: 0.654 AC: 1364 AN: 2086

Alfa AF: 0.643 Hom.: 43545

Bravo AF: 0.663

Asia WGS AF: 0.538 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		-0.12
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: rs173738; hg19: chr5-16725880;