NM_012334.3:c.1739+603C>T

Variant names:

• chr5-16760861-G-A
• rs31509
• NM_012334.3:c.1739+603C>T

Variant summary

Our verdict is Benign. The variant received -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
• 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=-1.0).
• 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 rank	MANE	Protein	UniProt
MYO10	NM_012334.3	c.1739+603C>T		intron_variant	Intron 17 of 40	ENST00000513610.6	NP_036466.2
MYO10	XM_006714475.4	c.1670+603C>T		intron_variant	Intron 16 of 39		XP_006714538.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO10	ENST00000513610.6	c.1739+603C>T		intron_variant	Intron 17 of 40	1	NM_012334.3	ENSP00000421280.1
MYO10	ENST00000274203.13	c.1739+603C>T		intron_variant	Intron 17 of 40	5		ENSP00000274203.10
MYO10	ENST00000513882.5	c.1772+603C>T		intron_variant	Intron 17 of 22	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

African (AFR) AF: 0.769 AC: 31882 AN: 41442

American (AMR) AF: 0.623 AC: 9502 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2431 AN: 3470

East Asian (EAS) AF: 0.676 AC: 3489 AN: 5164

South Asian (SAS) AF: 0.592 AC: 2854 AN: 4820

European-Finnish (FIN) AF: 0.769 AC: 8081 AN: 10504

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.713 AC: 48480 AN: 67968

Other (OTH) AF: 0.719 AC: 1521 AN: 2116

Alfa AF: 0.707 Hom.: 66704

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
PhyloP100		-0.95
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: rs31509; hg19: chr5-16760970;