NM_012334.3:c.21+12054C>T

Variant names:

• chr5-16923734-G-A
• rs2434960
• NM_012334.3:c.21+12054C>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.21+12054C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 150,764 control chromosomes in the GnomAD database, including 16,333 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 0.46 (16333 hom., cov: 30)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO10	NM_012334.3	c.21+12054C>T		intron_variant	Intron 1 of 40	ENST00000513610.6	NP_036466.2
MYO10	XM_006714475.4	c.21+12054C>T		intron_variant	Intron 1 of 39		XP_006714538.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO10	ENST00000513610.6	c.21+12054C>T		intron_variant	Intron 1 of 40	1	NM_012334.3	ENSP00000421280.1
MYO10	ENST00000507288.1	c.21+12054C>T		intron_variant	Intron 1 of 3	1		ENSP00000426664.1
MYO10	ENST00000274203.13	c.21+12054C>T		intron_variant	Intron 1 of 40	5		ENSP00000274203.10
MYO10	ENST00000502436.5	c.21+12054C>T		intron_variant	Intron 1 of 5	5		ENSP00000426783.2

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69279 AN: 150650 Hom.: 16327 Cov.: 30

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.460 AC: 69298 AN: 150764 Hom.: 16333 Cov.: 30 AF XY: 0.455 AC XY: 33449 AN XY: 73528

African (AFR) AF: 0.557 AC: 22832 AN: 40980

American (AMR) AF: 0.372 AC: 5614 AN: 15096

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1782 AN: 3464

East Asian (EAS) AF: 0.463 AC: 2360 AN: 5100

South Asian (SAS) AF: 0.509 AC: 2439 AN: 4794

European-Finnish (FIN) AF: 0.352 AC: 3589 AN: 10206

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29108 AN: 67830

Other (OTH) AF: 0.442 AC: 923 AN: 2088

Alfa AF: 0.442 Hom.: 58259

Bravo AF: 0.463

Asia WGS AF: 0.471 AC: 1637 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	1.2
DANN	Benign	0.42
PhyloP100		-2.0
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: rs2434960; hg19: chr5-16923843;