chr5-16713356-C-T

Variant names:

• chr5-16713356-C-T
• rs31299
• NM_012334.3:c.1930-2111G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012334.3(MYO10):​c.1930-2111G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 985,386 control chromosomes in the GnomAD database, including 312,907 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 0.76 (44796 hom., cov: 32)
  • Exomes 𝑓: 0.80 (268111 hom.)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO10	NM_012334.3	c.1930-2111G>A		intron_variant	Intron 19 of 40	ENST00000513610.6	NP_036466.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO10	ENST00000513610.6	c.1930-2111G>A		intron_variant	Intron 19 of 40	1	NM_012334.3	ENSP00000421280.1

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115902 AN: 151876 Hom.: 44777 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.779

GnomAD4 exome AF: 0.801 AC: 667674 AN: 833392 Hom.: 268111 Cov.: 44 AF XY: 0.800 AC XY: 308071 AN XY: 384914

African (AFR) AF: 0.638 AC: 10078 AN: 15786

American (AMR) AF: 0.792 AC: 779 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 4346 AN: 5152

East Asian (EAS) AF: 0.806 AC: 2923 AN: 3628

South Asian (SAS) AF: 0.622 AC: 10229 AN: 16448

European-Finnish (FIN) AF: 0.832 AC: 589 AN: 708

Middle Eastern (MID) AF: 0.736 AC: 1193 AN: 1620

European-Non Finnish (NFE) AF: 0.809 AC: 615895 AN: 761774

Other (OTH) AF: 0.793 AC: 21642 AN: 27292

GnomAD4 genome AF: 0.763 AC: 115967 AN: 151994 Hom.: 44796 Cov.: 32 AF XY: 0.763 AC XY: 56695 AN XY: 74276

African (AFR) AF: 0.656 AC: 27183 AN: 41406

American (AMR) AF: 0.789 AC: 12059 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2945 AN: 3470

East Asian (EAS) AF: 0.813 AC: 4196 AN: 5158

South Asian (SAS) AF: 0.639 AC: 3070 AN: 4802

European-Finnish (FIN) AF: 0.815 AC: 8608 AN: 10560

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55362 AN: 68004

Other (OTH) AF: 0.779 AC: 1648 AN: 2116

Alfa AF: 0.799 Hom.: 215416

Bravo AF: 0.758

Asia WGS AF: 0.703 AC: 2442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.29
PhyloP100		0.018
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs31299; hg19: chr5-16713465;