5-16922272-G-T

Position:

• chr5-16922272-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012334.3(MYO10):​c.21+13516C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 151,560 control chromosomes in the GnomAD database, including 48,814 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 0.80 (48814 hom., cov: 29)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO10	NM_012334.3	c.21+13516C>A		intron_variant		ENST00000513610.6	NP_036466.2
MYO10	XM_006714475.4	c.21+13516C>A		intron_variant			XP_006714538.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO10	ENST00000513610.6	c.21+13516C>A		intron_variant		1	NM_012334.3	ENSP00000421280.1
MYO10	ENST00000507288.1	c.21+13516C>A		intron_variant		1		ENSP00000426664.1
MYO10	ENST00000274203.13	c.21+13516C>A		intron_variant		5		ENSP00000274203.10
MYO10	ENST00000502436.5	c.21+13516C>A		intron_variant		5		ENSP00000426783.2

Frequencies

GnomAD3 genomes AF: 0.798 AC: 120864 AN: 151446 Hom.: 48777 Cov.: 29

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.835

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.798 AC: 120953 AN: 151560 Hom.: 48814 Cov.: 29 AF XY: 0.797 AC XY: 58962 AN XY: 73978

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.780

Alfa AF: 0.738 Hom.: 8081

Bravo AF: 0.807

Asia WGS AF: 0.834 AC: 2901 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	0.93
DANN	Benign	0.64

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: rs249120; hg19: chr5-16922381;