rs253336

Variant names:

• chr5-16840532-A-C
• rs253336
• NM_012334.3:c.121-22365T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-16840532-A-C
• chr5-16840532-A-G
• chr5-16840532-A-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.121-22365T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 151,984 control chromosomes in the GnomAD database, including 40,228 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 (40228 hom., cov: 31)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO10	NM_012334.3	c.121-22365T>G		intron_variant	Intron 2 of 40	ENST00000513610.6	NP_036466.2
MYO10	XM_006714475.4	c.121-22365T>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.121-22365T>G		intron_variant	Intron 2 of 40	1	NM_012334.3	ENSP00000421280.1

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110069 AN: 151866 Hom.: 40179 Cov.: 31

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.692

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.725 AC: 110176 AN: 151984 Hom.: 40228 Cov.: 31 AF XY: 0.724 AC XY: 53806 AN XY: 74270

African (AFR) AF: 0.795 AC: 32946 AN: 41460

American (AMR) AF: 0.745 AC: 11384 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2711 AN: 3468

East Asian (EAS) AF: 0.793 AC: 4081 AN: 5144

South Asian (SAS) AF: 0.556 AC: 2671 AN: 4802

European-Finnish (FIN) AF: 0.727 AC: 7692 AN: 10576

Middle Eastern (MID) AF: 0.690 AC: 200 AN: 290

European-Non Finnish (NFE) AF: 0.681 AC: 46270 AN: 67948

Other (OTH) AF: 0.741 AC: 1564 AN: 2110

Alfa AF: 0.701 Hom.: 69174

Bravo AF: 0.733

Asia WGS AF: 0.675 AC: 2348 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	0.021
DANN	Benign	0.65
PhyloP100		-2.1
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: rs253336; hg19: chr5-16840641;