chr5-16725771-A-G

Position:

• chr5-16725771-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

MYO10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO10	NM_012334.3	c.1930-14526T>C		intron_variant		ENST00000513610.6	NP_036466.2
MYO10	XM_006714475.4	c.1861-14526T>C		intron_variant			XP_006714538.1
MYO10	XM_005248307.3	c.1-14526T>C		intron_variant			XP_005248364.1
MYO10	XM_011514046.3	c.-1+12365T>C		intron_variant			XP_011512348.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO10	ENST00000513610.6	c.1930-14526T>C		intron_variant		1	NM_012334.3	ENSP00000421280.1

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

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.654

Alfa AF: 0.642 Hom.: 24626

Bravo AF: 0.663

Asia WGS AF: 0.538 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.61

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: rs173738; hg19: chr5-16725880;