rs25910

Variant names:

• chr5-16694200-T-C
• rs25910
• NM_012334.3:c.3800+171A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-16694200-T-C
• chr5-16694200-T-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.3800+171A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 152,122 control chromosomes in the GnomAD database, including 27,175 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 0.59 (27175 hom., cov: 33)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413
• Publications: 6 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 = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012334.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO10	NM_012334.3	MANE Select	c.3800+171A>G		intron	N/A	NP_036466.2	Q9HD67-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO10	ENST00000513610.6	TSL:1 MANE Select	c.3800+171A>G		intron	N/A	ENSP00000421280.1	Q9HD67-1
	MYO10	ENST00000274203.13	TSL:5	c.3833+171A>G		intron	N/A	ENSP00000274203.10	A0A0A0MQX1
	MYO10	ENST00000505695.5	TSL:2	c.1817+171A>G		intron	N/A	ENSP00000421170.1	E9PEW5

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89894 AN: 152004 Hom.: 27128 Cov.: 33

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.592 AC: 90004 AN: 152122 Hom.: 27175 Cov.: 33 AF XY: 0.594 AC XY: 44157 AN XY: 74346

African (AFR) AF: 0.707 AC: 29368 AN: 41518

American (AMR) AF: 0.580 AC: 8860 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1883 AN: 3470

East Asian (EAS) AF: 0.543 AC: 2799 AN: 5156

South Asian (SAS) AF: 0.557 AC: 2684 AN: 4820

European-Finnish (FIN) AF: 0.614 AC: 6490 AN: 10576

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 35999 AN: 67978

Other (OTH) AF: 0.592 AC: 1252 AN: 2114

Alfa AF: 0.549 Hom.: 71157

Bravo AF: 0.595

Asia WGS AF: 0.554 AC: 1927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.61
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs25910; hg19: chr5-16694309; COSMIC: COSV57022489;