rs31509

Positions:

• chr5-16760861-G-A
• chr5-16760861-G-C

Variant summary

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

The NM_012334.3(MYO10):​c.1739+603C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,942 control chromosomes in the GnomAD database, including 39,472 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 0.72 (39472 hom., cov: 31)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946

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 = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO10	NM_012334.3	c.1739+603C>T		intron_variant		ENST00000513610.6	NP_036466.2
MYO10	XM_006714475.4	c.1670+603C>T		intron_variant			XP_006714538.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO10	ENST00000513610.6	c.1739+603C>T		intron_variant		1	NM_012334.3	ENSP00000421280.1
MYO10	ENST00000274203.13	c.1739+603C>T		intron_variant		5		ENSP00000274203.10
MYO10	ENST00000513882.5	c.1772+603C>T		intron_variant		2		ENSP00000421309.1

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109043 AN: 151826 Hom.: 39440 Cov.: 31

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.718 AC: 109122 AN: 151942 Hom.: 39472 Cov.: 31 AF XY: 0.717 AC XY: 53226 AN XY: 74262

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.719

Alfa AF: 0.706 Hom.: 48513

Bravo AF: 0.712

Asia WGS AF: 0.612 AC: 2133 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	0.20
DANN	Benign	0.58

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: rs31509; hg19: chr5-16760970;