chr5-16875581-T-C

Variant names:

• chr5-16875581-T-C
• rs2625210
• NM_012334.3:c.120+2028A>G

Variant summary

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

The NM_012334.3(MYO10):​c.120+2028A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,034 control chromosomes in the GnomAD database, including 41,386 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 0.74 (41386 hom., cov: 31)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO10	NM_012334.3	c.120+2028A>G		intron_variant	Intron 2 of 40	ENST00000513610.6	NP_036466.2
MYO10	XM_006714475.4	c.120+2028A>G		intron_variant	Intron 2 of 39		XP_006714538.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO10	ENST00000513610.6	c.120+2028A>G		intron_variant	Intron 2 of 40	1	NM_012334.3	ENSP00000421280.1

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111650 AN: 151916 Hom.: 41316 Cov.: 31

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.735 AC: 111781 AN: 152034 Hom.: 41386 Cov.: 31 AF XY: 0.733 AC XY: 54463 AN XY: 74298

African (AFR) AF: 0.806 AC: 33455 AN: 41500

American (AMR) AF: 0.753 AC: 11505 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2243 AN: 3470

East Asian (EAS) AF: 0.643 AC: 3314 AN: 5150

South Asian (SAS) AF: 0.717 AC: 3450 AN: 4812

European-Finnish (FIN) AF: 0.705 AC: 7425 AN: 10532

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48254 AN: 67978

Other (OTH) AF: 0.726 AC: 1533 AN: 2112

Alfa AF: 0.713 Hom.: 157953

Bravo AF: 0.740

Asia WGS AF: 0.754 AC: 2620 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	0.27
DANN	Benign	0.61
PhyloP100		-2.3
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: rs2625210; hg19: chr5-16875690;