rs40979

Positions:

• chr5-16721197-A-C
• chr5-16721197-A-G
• chr5-16721197-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.1930-9952T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,130 control chromosomes in the GnomAD database, including 53,384 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 0.84 (53384 hom., cov: 32)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO10	NM_012334.3	c.1930-9952T>G		intron_variant		ENST00000513610.6
MYO10	XM_005248307.3	c.1-9952T>G		intron_variant
MYO10	XM_006714475.4	c.1861-9952T>G		intron_variant
MYO10	XM_011514046.3	c.1-9952T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO10	ENST00000513610.6	c.1930-9952T>G		intron_variant		1	NM_012334.3	P1

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127059 AN: 152012 Hom.: 53351 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.836 AC: 127144 AN: 152130 Hom.: 53384 Cov.: 32 AF XY: 0.836 AC XY: 62188 AN XY: 74354

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.902

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.857

Gnomad4 OTH AF: 0.838

Alfa AF: 0.851 Hom.: 111527

Bravo AF: 0.831

Asia WGS AF: 0.749 AC: 2603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.46

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: rs40979; hg19: chr5-16721306;